Contacts of the helix formed by residues 106 - 127 (chain C) in PDB entry 2PK9
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 GLU 106 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C LEU* 1.3 73.1 - - - +
107C LEU* 1.3 64.5 + - - +
108C ASN* 3.1 23.6 + - - +
109C LEU* 3.2 24.9 + - + +
110C VAL* 3.2 13.4 + - - +
264C GLU* 3.3 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C LEU 4.4 4.3 - - - +
106C GLU* 1.3 71.6 - - - +
108C ASN* 1.3 60.0 + - - +
110C VAL* 3.8 12.0 - - + +
111C LYS* 3.3 25.6 + - - +
203C ILE* 4.7 7.6 - - + -
262C THR* 3.9 10.3 - - - +
264C GLU* 2.8 35.9 + - + +
265C PRO 3.5 24.5 - - - +
266C LEU* 3.9 27.1 - - + -
267C ASP* 5.5 3.1 - - - +
270C LEU* 4.2 16.8 - - + -
296C TRP* 4.6 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C GLU* 3.1 19.0 + - - +
107C LEU* 1.3 76.3 - - - +
109C LEU* 1.3 62.9 + - - +
111C LYS* 3.6 10.1 + - - +
112C TYR* 3.2 22.3 + - - +
299C GLU* 4.3 13.7 - - - +
300C TYR* 5.1 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C TYR* 3.9 25.4 - - + +
105C LEU* 4.7 16.6 - - + -
106C GLU* 3.2 19.8 + - + +
108C ASN* 1.3 76.4 - - - +
110C VAL* 1.3 64.7 + - - +
112C TYR* 3.5 14.6 + - + +
113C PHE* 3.1 63.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C LEU* 3.8 24.9 - - + +
106C GLU 3.2 21.3 + - - +
107C LEU* 3.8 12.6 - - + +
109C LEU* 1.3 73.9 - - - +
111C LYS* 1.3 60.3 + - - +
113C PHE 3.2 1.7 + - - -
114C GLN* 2.8 30.9 + - - +
199C LEU* 4.2 21.3 - - + -
202C MET* 3.4 45.5 - - + +
203C ILE* 4.4 10.8 - - + +
296C TRP* 4.8 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C LEU 3.3 14.9 + - - +
108C ASN* 3.7 11.7 + - - +
110C VAL* 1.3 78.4 - - - +
112C TYR* 1.3 54.4 + - - +
114C GLN* 3.1 2.4 + - - +
115C TRP* 2.7 35.4 + - - +
296C TRP* 3.5 65.9 + - + +
297C PHE* 3.8 14.9 - - + -
299C GLU* 2.8 38.1 + - - +
300C TYR* 3.9 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ASN 3.2 15.5 + - - +
109C LEU* 3.7 16.8 - - + +
111C LYS* 1.3 78.6 - - - +
113C PHE* 1.3 72.8 + + - +
115C TRP* 3.4 11.4 - + - +
116C GLN* 2.8 51.9 + - + +
144C ARG 5.5 0.7 + - - -
145C GLY* 3.3 29.4 + - - -
146C GLN* 4.6 4.7 + - - +
300C TYR* 4.1 27.1 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C LEU* 4.5 5.8 - - + -
92C TYR* 3.9 33.2 - + - -
105C LEU* 4.4 6.7 - - + -
109C LEU* 3.1 45.6 + - + +
110C VAL 3.8 2.7 - - - +
112C TYR* 1.3 82.7 - + - +
114C GLN* 1.3 56.0 + - - +
116C GLN* 3.1 17.0 + - - +
117C LEU* 2.7 35.7 + - - +
141C ILE* 4.4 18.2 - - + -
145C GLY* 3.5 25.4 - - - -
147C LEU* 3.8 23.9 - - + +
202C MET* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C VAL 2.8 18.2 + - - +
111C LYS 3.5 4.7 - - - +
113C PHE* 1.3 72.0 - - - +
115C TRP* 1.3 65.5 + - - +
117C LEU* 3.5 14.3 + - - +
118C LEU* 3.1 38.0 + - + +
195C CYS* 3.1 28.7 + - - +
199C LEU* 3.4 39.4 + - + +
202C MET* 3.2 21.6 - - + +
273C PHE* 4.2 0.7 - - + -
277C LEU* 3.6 12.9 - - - +
296C TRP* 4.2 16.2 - - + -
297C PHE* 4.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C LYS 2.7 19.9 + - - +
112C TYR* 3.4 16.4 - + - +
114C GLN* 1.3 71.8 - - - +
116C GLN* 1.3 63.8 + - + +
118C LEU* 3.2 3.4 + - - +
119C GLN* 2.8 65.7 + - + +
292C LEU* 4.1 24.9 - - + +
297C PHE* 3.7 50.6 - + + -
300C TYR* 3.9 47.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ASN* 3.5 33.0 - - - +
112C TYR* 2.8 53.3 + - - +
113C PHE* 3.1 28.4 + - - +
115C TRP* 1.3 88.6 - - + +
117C LEU* 1.3 62.4 + - - +
120C GLY* 3.3 17.3 + - - -
145C GLY 3.6 2.1 + - - +
146C GLN* 3.7 7.3 - - - +
147C LEU* 3.4 35.4 - - + +
149C LEU* 5.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C PHE 2.7 19.5 + - - +
114C GLN* 3.8 19.3 - - - +
116C GLN* 1.3 73.1 - - - +
118C LEU* 1.3 58.2 - - + +
121C LEU* 3.3 27.3 + - + +
134C LEU* 4.5 8.7 - - + -
139C LEU* 3.4 31.2 - - + -
147C LEU* 3.5 11.4 - - + +
149C LEU* 3.9 16.9 - - + +
195C CYS* 4.0 29.6 - - + -
198C ILE* 3.8 37.0 - - + -
202C MET* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C GLN* 3.1 33.4 + - + +
117C LEU* 1.3 76.0 - - + +
119C GLN* 1.3 58.2 + - - +
121C LEU* 3.6 2.8 - - + +
122C ALA* 2.6 37.2 + - - +
192C ILE* 4.3 14.8 - - + -
195C CYS* 4.1 26.9 - - + -
273C PHE* 3.7 16.6 - - + -
277C LEU* 5.1 3.4 - - + -
288C ALA* 4.3 7.3 - - + +
291C ALA* 3.9 19.1 - - + -
292C LEU* 3.6 16.8 - - + -
297C PHE* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C HIS* 3.7 19.9 + - + +
63C GLU* 5.9 1.3 - - - +
64C ASN* 3.2 18.8 - - - +
115C TRP* 2.8 57.9 + - - +
116C GLN* 4.0 0.9 - - - +
118C LEU* 1.3 75.3 - - - +
120C GLY* 1.3 62.2 + - - +
122C ALA* 3.5 5.0 + - - +
123C PHE* 3.3 14.6 + - - +
292C LEU* 3.6 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C HIS* 3.8 8.5 - - - -
64C ASN* 3.5 24.0 + - - -
65C ILE* 3.9 2.0 - - - +
116C GLN 3.3 9.4 + - - -
119C GLN* 1.3 76.9 - - - +
121C LEU* 1.3 62.1 + - - +
123C PHE* 3.1 8.1 + - - +
124C CYS* 3.1 22.0 + - - -
149C LEU* 3.5 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C LEU 3.3 18.0 + - - +
118C LEU* 3.2 8.4 + - + +
120C GLY* 1.3 72.3 - - - +
122C ALA* 1.3 55.2 + - - +
124C CYS* 2.9 14.8 + - + +
125C HIS* 2.8 56.6 + - + +
131C HIS* 4.7 5.8 - - + -
134C LEU* 3.9 11.7 - - + -
149C LEU* 3.5 9.2 - - + +
191C ASP* 3.4 35.9 - - + +
192C ILE* 4.2 10.3 - - + -
195C CYS* 3.3 34.5 - - - -
288C ALA* 4.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU 2.6 21.6 + - - +
119C GLN* 3.5 8.1 - - - +
121C LEU* 1.3 72.2 - - - +
123C PHE* 1.3 56.2 + - - +
125C HIS* 3.5 3.6 + - - +
126C GLU* 3.0 29.8 + - - +
288C ALA* 3.7 22.5 - - + +
289C LYS* 4.6 4.5 - - + +
292C LEU* 3.8 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLU 4.0 5.4 - - - -
60C LEU* 3.6 26.2 - - + -
61C LYS 3.9 30.5 - - - -
62C HIS* 3.4 36.1 - + + +
65C ILE* 3.7 8.3 - - + -
119C GLN 3.3 5.1 + - - +
120C GLY 3.1 11.1 + - - +
121C LEU 3.1 0.6 - - - -
122C ALA* 1.3 74.6 - - - +
124C CYS* 1.3 67.3 + - - +
126C GLU* 3.2 6.3 + - + +
127C ASN* 3.1 47.7 + - - +
207D VAL* 6.0 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C LEU* 3.8 19.3 - - + -
65C ILE* 4.0 5.6 - - - -
120C GLY 3.1 16.6 + - - -
121C LEU* 2.9 18.3 + - + +
123C PHE* 1.3 78.7 - - - +
125C HIS* 1.3 60.3 + - - +
127C ASN* 3.4 2.6 + - - -
128C LYS 3.4 3.3 + - - -
129C ILE* 2.8 39.9 + - - +
130C LEU* 5.6 0.4 - - - -
131C HIS* 5.7 2.0 - - - +
149C LEU* 3.7 15.9 - - - -
152C PHE* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LEU* 2.8 46.7 + - + +
122C ALA* 4.0 5.4 - - - +
124C CYS* 1.3 71.3 - - - +
126C GLU* 1.3 62.2 + - - +
128C LYS* 3.0 21.2 + - - +
129C ILE 3.8 10.0 + - - +
130C LEU* 4.0 9.7 - - + +
188C THR* 3.2 61.3 + - + +
191C ASP* 3.3 23.6 - - - +
192C ILE* 4.6 2.9 - - + +
288C ALA* 4.0 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ALA 3.0 19.1 + - - +
123C PHE* 3.7 8.7 - - + +
125C HIS* 1.3 77.6 - - - +
127C ASN* 1.3 65.0 + - - +
128C LYS* 3.2 5.1 + - - +
289C LYS* 5.9 2.9 - - - +
206D TYR 5.0 0.7 - - - +
207D VAL* 5.0 22.9 - - + -
208D ASN 5.0 3.6 + - - -
212D SER* 3.0 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLU 3.8 9.9 - - - +
60C LEU* 4.4 2.7 - - + -
123C PHE* 3.1 44.8 + - - +
124C CYS 3.4 4.0 + - - +
125C HIS 3.1 0.2 - - - -
126C GLU* 1.3 86.7 - - - +
128C LYS* 1.3 61.8 + - - +
129C ILE* 3.2 19.3 + - + +
173D ARG* 2.9 35.4 + - - +
206D TYR* 4.7 6.4 + - - +
207D VAL* 6.0 3.4 - - - +
212D SER* 4.8 0.4 + - - -
214D TYR* 3.0 23.9 + - - -
----------------------------------------------------------
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