Contacts of the helix formed by residues 101 - 122 (chain K) in PDB entry 4HOK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 101 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I ARG* 3.4 37.9 + - - -
100K PHE* 1.3 73.6 - - - +
102K LEU* 1.3 64.1 + - - +
103K LYS* 3.7 8.9 + - - +
104K THR* 3.2 9.5 + - - -
105K VAL* 3.0 23.7 + - - +
207K ASN* 5.3 0.2 - - - -
289K ASP* 2.7 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101K SER* 1.3 72.9 - - - +
103K LYS* 1.3 65.1 + - - +
105K VAL* 3.3 4.5 + - + -
106K LEU* 2.9 45.6 + - + +
207K ASN* 4.6 6.9 + - - +
244K TYR* 5.8 1.6 - - + -
245K PRO* 3.7 26.5 - - + -
248K PHE* 3.7 35.7 - - + -
276K LEU* 4.4 5.8 - - + -
280K GLN* 3.6 28.7 - - - +
282K PHE* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 103 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I ARG* 6.1 0.7 - - - +
34I GLU* 3.5 28.0 + - - +
101K SER* 3.2 9.4 + - - +
102K LEU* 1.3 79.4 - - - +
104K THR* 1.3 63.5 + - - +
106K LEU* 3.4 2.5 + - - +
107K LEU* 3.1 36.4 + - + +
277K PHE* 4.0 12.6 - - + -
282K PHE* 3.8 39.8 - - + -
283K SER* 3.4 23.9 + - - +
285K ASP* 2.9 29.1 + - - -
287K VAL* 4.0 16.2 + - - +
289K ASP* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 104 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100K PHE* 3.6 20.9 - - + -
101K SER* 3.2 10.5 + - - -
103K LYS* 1.3 78.7 - - - +
105K VAL* 1.3 65.6 + - - +
107K LEU* 3.2 11.5 + - - +
108K LEU* 2.9 44.5 + - + +
287K VAL 4.7 0.5 + - - -
288K PHE* 3.4 8.5 - - + -
289K ASP* 2.9 40.7 + - - -
290K TRP* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100K PHE* 3.8 19.5 - - + +
101K SER 3.0 17.0 + - - +
102K LEU* 3.5 8.3 - - + +
104K THR* 1.3 77.8 - - - +
106K LEU* 1.3 59.8 + - + +
108K LEU* 3.1 8.8 + - - +
109K ALA* 2.7 27.8 + - + +
203K LEU* 4.4 19.1 - - + +
206K PHE* 4.1 12.1 - - + -
207K ASN* 3.1 31.2 - - - +
248K PHE* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102K LEU* 2.9 35.2 + - + +
103K LYS 3.8 3.6 - - - +
105K VAL* 1.3 73.6 - - - +
107K LEU* 1.3 64.3 + - - +
109K ALA* 3.2 4.8 + - + +
110K ASP* 3.0 23.9 + - - +
248K PHE* 4.1 11.4 - - + -
273K PHE* 3.4 44.0 - - + +
276K LEU* 3.8 30.7 - - + -
277K PHE* 3.8 34.3 - - + +
282K PHE* 4.2 8.3 - - + -
284K TYR* 5.6 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103K LYS* 3.1 36.9 + - + +
104K THR* 3.2 9.6 + - - +
106K LEU* 1.3 75.9 - - - +
108K LEU* 1.3 64.4 + - - +
110K ASP* 3.6 15.8 + - - +
111K GLN* 3.7 14.3 + - - +
277K PHE* 3.9 12.1 - - + -
284K TYR* 3.8 36.3 - - + -
286K TYR* 4.2 33.4 - - + +
287K VAL 4.7 2.0 - - - +
288K PHE* 3.6 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89K LEU* 4.2 15.0 - - + -
100K PHE* 3.8 22.7 - - + -
104K THR* 2.9 40.1 + - + +
105K VAL* 3.6 3.8 - - - +
107K LEU* 1.3 73.7 - - - +
109K ALA* 1.3 66.1 + - - +
111K GLN* 3.3 3.1 + - - +
112K MET* 2.9 40.8 + - - +
136K MET* 4.5 0.9 - - - -
145K VAL* 3.8 26.5 - - + -
203K LEU* 5.4 0.2 - - + -
206K PHE* 4.1 14.6 - - + -
288K PHE* 4.2 9.6 - - + -
290K TRP* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105K VAL* 2.7 21.2 + - + +
106K LEU* 3.5 10.1 - - + +
108K LEU* 1.3 74.1 - - - +
110K ASP* 1.3 66.6 + - - +
112K MET* 4.1 3.0 - - - +
113K ILE* 3.2 28.2 + - + +
199K LEU* 5.5 0.7 - - - -
203K LEU* 3.9 34.2 - - + +
273K PHE* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106K LEU 3.0 12.0 + - - +
107K LEU* 3.6 12.1 - - - +
108K LEU 3.3 0.2 - - - -
109K ALA* 1.3 79.0 - - - +
111K GLN* 1.3 70.1 + - + +
113K ILE* 3.5 5.2 + - - +
114K SER* 3.5 18.5 + - - -
270K ARG* 3.9 29.7 - - - +
273K PHE* 5.4 3.5 - - + +
274K ARG* 3.8 26.3 + - - +
284K TYR* 4.6 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 111 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107K LEU 3.7 10.8 + - - +
108K LEU* 3.3 6.2 + - - +
110K ASP* 1.3 84.2 - - + +
112K MET* 1.3 58.2 + - - +
114K SER* 2.7 31.8 + - - -
115K ARG* 2.5 47.7 + - - +
143K ASN 2.9 25.6 + - - -
144K LEU* 3.5 7.6 - - - +
145K VAL* 2.8 35.8 + - + +
286K TYR* 4.5 13.9 + - + -
288K PHE* 5.0 4.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 112 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89K LEU* 3.8 13.5 - - + -
108K LEU* 2.9 42.0 + - + +
109K ALA 4.1 2.2 - - - +
111K GLN* 1.3 71.7 - - - +
113K ILE* 1.3 61.8 + - - +
115K ARG* 3.6 9.5 + - - +
116K ILE* 3.1 30.1 + - - +
134K PHE* 3.1 55.8 - - + -
145K VAL* 4.3 10.7 - - + +
199K LEU* 3.9 29.8 - - + -
202K VAL* 4.1 14.1 - - + -
203K LEU* 4.5 4.9 - - - -
206K PHE* 4.4 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109K ALA* 3.2 19.8 + - + +
110K ASP 3.8 4.3 - - - +
111K GLN 3.1 1.0 - - - -
112K MET* 1.3 76.4 - - - +
114K SER* 1.3 53.5 + - - +
116K ILE* 3.3 4.6 + - - +
117K GLU* 2.7 32.6 + - - +
196K LEU* 4.3 7.4 - - + -
199K LEU* 3.4 21.1 - - + -
251K TYR* 3.9 25.6 - - + +
266K TYR* 4.1 38.8 - - + +
269K LEU* 4.1 22.0 - - + -
270K ARG* 4.3 11.2 - - + +
273K PHE* 4.3 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110K ASP* 3.5 7.9 + - - -
111K GLN* 2.7 21.3 + - - -
113K ILE* 1.3 74.0 - - - +
115K ARG* 1.3 71.4 + - - -
117K GLU* 3.2 8.8 + - - +
118K TYR* 2.9 29.0 + - - +
270K ARG* 3.3 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K VAL* 3.6 36.3 + - - +
64K GLY* 3.8 8.6 - - - -
65K ILE* 5.6 1.8 - - + -
111K GLN* 2.5 51.3 + - - +
112K MET* 3.9 8.1 - - - +
114K SER* 1.3 93.5 - - - +
116K ILE* 1.3 68.8 + - - +
118K TYR* 3.1 9.4 + - - +
119K ILE* 3.1 27.5 + - - +
134K PHE* 4.8 1.6 - - + -
144K LEU* 3.6 17.4 - - - +
145K VAL* 2.6 30.2 + - + +
146K TYR 4.9 0.2 - - - -
147K ILE* 4.0 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 116 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112K MET 3.1 18.4 + - - +
113K ILE* 3.6 4.9 - - - +
115K ARG* 1.3 81.2 - - - +
117K GLU* 1.3 65.6 + - - +
119K ILE* 3.5 8.6 + - - +
120K HIS* 3.2 47.2 + - + +
126K HIS* 5.9 1.8 - - + -
129K VAL* 3.8 36.3 - - + -
134K PHE* 4.5 3.8 - - + -
147K ILE* 4.5 15.0 - - + +
195K ASP* 3.8 14.4 - - + +
196K LEU* 4.1 12.3 - - + -
199K LEU* 4.1 20.6 - - + -
266K TYR* 4.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 117 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113K ILE 2.7 20.0 + - - +
114K SER* 3.4 6.8 - - - +
116K ILE* 1.3 71.7 - - - +
118K TYR* 1.3 65.8 + - - +
120K HIS* 2.8 8.3 + - - +
121K SER* 2.8 22.9 + - - -
266K TYR* 2.8 56.0 - - + +
267K SER 4.9 0.5 + - - -
270K ARG* 2.5 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59K MET* 2.9 32.8 + - - -
60K GLN 3.7 4.0 + - - -
61K GLY 3.8 0.7 - - - -
62K GLY* 2.8 44.0 + - - -
63K VAL 4.5 8.3 - - - +
65K ILE* 3.9 19.5 - - + -
114K SER 2.9 12.9 + - - +
115K ARG* 3.3 11.9 - - - +
117K GLU* 1.3 74.3 - - - +
119K ILE* 1.3 61.2 + - + +
121K SER* 2.5 41.7 + - - -
122K LYS* 3.0 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59K MET* 4.0 22.4 - - + -
65K ILE* 5.0 0.7 - - + -
115K ARG 3.1 9.9 + - - +
116K ILE* 3.7 7.6 - - - +
118K TYR* 1.3 85.8 - - + +
120K HIS* 1.3 57.3 + - + +
122K LYS* 2.7 33.9 + - - +
124K PHE* 3.1 28.8 + - + +
125K ILE 4.2 9.4 - - - +
126K HIS* 4.0 10.3 - - + +
147K ILE* 3.4 40.8 - - + -
150K PHE* 3.4 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 120 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116K ILE* 3.2 28.0 + - + +
117K GLU 2.8 10.7 + - - +
119K ILE* 1.3 79.1 - - + +
121K SER* 1.3 63.1 + - - +
123K ASN 3.0 8.7 + - - -
124K PHE 3.2 18.8 - - - -
125K ILE* 4.0 3.3 - - - +
156K TYR* 2.6 23.1 + - - +
157K ARG* 4.0 1.0 - - - -
192K ARG* 3.0 53.2 - - + +
195K ASP* 2.7 26.9 + - - -
196K LEU* 4.8 2.0 - - + -
266K TYR* 2.7 31.9 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 121 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117K GLU* 2.8 15.3 + - - -
118K TYR* 2.5 28.3 + - - -
120K HIS* 1.3 76.8 - - - +
122K LYS* 1.3 70.9 + - - +
123K ASN* 3.2 2.8 - - - +
157K ARG* 3.0 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58K MET* 4.8 17.1 + - + +
59K MET* 4.2 15.5 - - + -
60K GLN 5.1 3.2 + - - -
118K TYR* 3.0 58.1 + - + +
119K ILE 2.7 9.5 + - - +
121K SER* 1.3 82.6 - - - +
123K ASN* 1.3 69.2 + - - +
124K PHE* 3.2 23.2 + - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il