Contacts of the helix formed by residues 98 - 112 (chain K) in PDB entry 3KC3
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 CYS 98 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96K GLN 4.0 4.9 - - - -
97K ASP* 1.3 91.1 + - - +
99K PRO* 1.3 78.8 - - + +
100K LYS* 3.8 13.5 - - - -
101K ALA* 3.0 32.8 + - - +
102K ARG* 3.2 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 99 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98K CYS* 1.3 83.6 - - + +
100K LYS* 1.3 65.5 + - - +
102K ARG* 2.8 22.2 + - + +
103K ARG* 3.1 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98K CYS* 3.2 12.8 + - - -
99K PRO* 1.3 77.0 - - - +
101K ALA* 1.3 56.0 + - - +
103K ARG* 3.3 31.5 - - - +
104K GLU* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95K LEU* 4.4 17.0 - - + +
96K GLN 3.6 23.3 - - - +
98K CYS* 3.0 19.0 + - - +
100K LYS* 1.3 72.7 - - - +
102K ARG* 1.3 56.6 + - - +
103K ARG 3.1 4.9 - - - -
104K GLU* 3.7 7.3 - - - +
105K VAL* 3.0 35.3 + - - +
134K LEU* 4.1 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K ILE* 3.6 29.5 - - - +
97K ASP* 3.3 38.4 + - - +
98K CYS 3.9 5.8 - - - +
99K PRO* 2.8 15.9 + - + +
101K ALA* 1.3 73.7 - - - +
103K ARG* 1.3 57.6 + - - +
105K VAL* 4.0 4.4 - - - +
106K GLU* 2.9 27.3 + - - +
125K GLU* 3.5 31.5 + - - +
132K LYS* 5.3 2.2 - - - +
134K LEU* 3.8 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K PRO* 3.1 23.2 + - - +
100K LYS* 3.3 42.1 - - - +
102K ARG* 1.3 74.8 - - - +
104K GLU* 1.3 59.0 + - - +
105K VAL 3.1 1.3 - - - -
106K GLU* 2.9 8.0 + - + +
107K LEU* 2.7 56.6 + - + +
211K ALA 4.7 7.9 + - - +
212K LYS* 5.7 11.2 - - - +
213K GLU* 4.4 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74K ILE* 4.6 1.2 - - - +
93K LYS* 2.8 32.9 + - - +
95K LEU* 3.3 24.4 - - + +
100K LYS 2.9 17.3 + - - +
101K ALA* 3.3 8.7 + - - +
103K ARG* 1.3 75.8 - - - +
105K VAL* 1.3 64.0 + - - +
107K LEU* 4.2 4.4 - - - +
108K HIS* 3.1 26.0 + - - +
136K ILE* 3.8 13.7 - - - +
208K PHE* 3.4 34.6 + - + +
209K GLY* 3.2 18.9 - - - -
500K MK2 5.7 0.7 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
52K LEU* 3.6 28.3 - - + -
54K ILE* 5.6 3.8 - - + -
95K LEU* 5.3 1.8 - - + -
101K ALA 3.0 17.5 + - - +
102K ARG* 4.0 7.0 - - - +
104K GLU* 1.3 74.1 - - + +
106K GLU* 1.3 59.2 + - + +
108K HIS* 2.8 8.1 + - - +
109K TRP* 2.7 32.5 + - + +
120K ILE* 4.6 2.4 - - + +
123K VAL* 4.4 17.0 - - + -
134K LEU* 3.8 20.9 - - + -
136K ILE* 4.0 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J LYS* 3.1 49.8 + - - +
52K LEU* 5.3 2.0 - - - -
102K ARG 2.9 20.2 + - - +
103K ARG* 2.9 8.7 + - + +
105K VAL* 1.3 83.2 - - + +
107K LEU* 1.3 74.0 + - + +
109K TRP* 3.5 11.0 + - - +
110K ARG* 3.2 36.3 + - - +
213K GLU* 5.4 5.5 - - - +
----------------------------------------------------------
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 ARG* 2.7 38.4 + - + +
104K GLU* 4.2 4.9 - - - +
106K GLU* 1.3 74.6 - - + +
108K HIS* 1.3 55.9 + - - +
110K ARG* 2.7 56.2 + - - +
111K ALA* 3.1 11.1 + - - +
182K ILE* 4.0 17.9 - - + +
208K PHE* 4.6 4.3 - - + -
211K ALA* 3.6 45.8 - - + +
212K LYS* 3.9 9.9 - - - +
213K GLU* 3.9 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 108 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104K GLU* 3.1 23.2 + - - +
105K VAL* 2.8 6.7 + - - +
107K LEU* 1.3 74.8 - - - +
109K TRP* 1.3 63.8 + - - +
111K ALA* 3.0 12.7 + - - +
112K SER* 3.0 12.1 + - - -
117K ILE* 4.6 2.0 - - + -
118K VAL* 3.0 38.5 + - + +
120K ILE* 3.4 25.2 - - + +
136K ILE* 5.3 4.7 - - + +
138K MET* 4.1 8.3 - - - -
208K PHE* 3.2 45.5 + + + +
500K MK2 3.8 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 109 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127J LEU* 3.9 15.5 - - + +
49K LYS* 6.0 2.5 - - + -
50K SER* 3.0 32.3 + - - -
51K GLY* 3.3 19.9 - - - -
52K LEU* 3.6 56.6 - - + +
105K VAL 2.7 19.3 + - - +
106K GLU* 3.7 11.4 - - - +
108K HIS* 1.3 74.4 - - - +
110K ARG* 1.3 68.5 + - + +
112K SER* 3.0 26.6 + - - -
113K GLN* 4.2 1.6 + - - +
120K ILE* 4.0 35.6 - - + +
121K VAL 5.2 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 110 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127J LEU* 4.2 25.9 - - + +
130J GLY* 2.6 37.5 + - - +
131J ARG* 4.4 9.1 - - - +
132J LYS* 4.6 11.9 - - + +
106K GLU* 3.2 35.3 + - - +
107K LEU* 2.7 23.0 + - - +
109K TRP* 1.3 80.1 - - + +
111K ALA* 1.3 61.0 + - - +
112K SER 3.5 0.5 + - - -
113K GLN* 3.9 5.9 + - - +
176K TYR* 3.7 20.4 + - - -
180K ILE* 3.3 45.7 + - + +
181K ASN* 4.8 0.6 + - - +
182K ILE* 4.1 6.3 - - + +
213K GLU* 3.7 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107K LEU 3.1 6.3 + - - +
108K HIS 3.0 11.1 + - - +
110K ARG* 1.3 75.0 - - - +
112K SER* 1.3 62.2 + - - +
113K GLN 3.0 5.3 + - - -
114K CYS* 3.1 21.4 + - - +
117K ILE* 3.8 13.7 - - + +
176K TYR* 4.3 8.1 - - - -
177K LEU* 3.8 19.1 - - + -
180K ILE* 4.6 1.3 - - + +
182K ILE* 5.3 0.9 - - + +
208K PHE* 3.5 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108K HIS* 3.0 12.5 + - - -
109K TRP* 3.0 22.3 + - - -
111K ALA* 1.3 76.3 - - - +
113K GLN* 1.3 60.9 + - - +
114K CYS 3.2 7.1 + - - +
117K ILE* 4.9 5.2 - - - -
118K VAL 4.1 2.3 + - - -
119K ARG* 3.5 29.0 - - - +
120K ILE* 2.8 43.2 + - - +
----------------------------------------------------------
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