Contacts of the helix formed by residues 60 - 72 (chain B) in PDB entry 6XWQ
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 VAL 60 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASN* 5.6 2.9 - - - +
56B LEU 4.3 1.3 - - - +
57B LYS* 3.3 16.8 - - + +
58B MET 3.4 1.2 - - - -
59B LEU* 1.3 79.2 - - - +
61B MET* 1.3 77.1 + - + +
64B VAL* 3.1 28.5 + - + +
153B VAL* 5.2 5.0 - - + +
281B SER* 3.5 27.1 + - - +
311B THR* 5.9 3.8 - - + -
356B ALA* 4.2 11.7 - - + -
357B GLY 3.8 19.3 - - - +
358B VAL* 3.8 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASN* 3.3 25.8 + - - +
145A PHE* 3.9 9.6 - - + -
58B MET 4.6 0.2 + - - -
60B VAL* 1.3 85.3 - - + +
62B PRO* 1.3 69.3 - - + +
64B VAL* 3.1 8.4 - - - +
65B LEU* 3.0 25.3 + - - +
148B LEU* 3.9 24.2 - - + +
151B GLY* 3.3 38.4 - - - +
152B GLU 3.8 1.8 - - - +
153B VAL* 3.7 19.5 - - + -
156B VAL* 3.6 35.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PRO* 3.6 28.3 - - + -
145A PHE* 4.2 22.2 - - + -
159A PHE* 4.7 1.8 - - + -
58B MET 3.5 17.3 - - - +
59B LEU 4.5 0.2 - - - -
60B VAL 4.0 1.8 - - - +
61B MET* 1.3 94.5 - - + +
63B ILE* 1.3 62.0 + - - +
65B LEU* 3.9 2.4 - - + +
66B ALA* 2.9 30.2 + - - +
192B LEU* 5.0 6.8 - - + +
196B MET* 3.6 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 3.1 31.9 - - + +
60B VAL 4.6 0.9 - - - +
61B MET 3.3 0.4 - - - -
62B PRO* 1.3 78.7 - - - +
64B VAL* 1.3 65.7 + - - +
66B ALA* 5.1 1.1 - - - -
67B SER* 2.9 32.6 + - - +
193B ALA* 5.8 1.1 - - - +
196B MET* 3.5 28.7 - - + +
197B TYR* 4.4 17.0 - - + -
200B VAL* 3.5 31.4 - - + -
281B SER* 4.1 11.7 - - - +
284B LEU* 3.5 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL 3.1 18.6 + - - +
61B MET* 3.1 29.4 + - + +
63B ILE* 1.3 80.2 - - + +
65B LEU* 1.3 68.4 + - - +
67B SER* 5.0 0.4 - - - -
68B LEU* 2.9 45.7 + - + +
153B VAL* 4.9 6.3 - - + -
156B VAL* 4.0 7.2 - - + -
157B ILE* 3.5 29.6 - - + -
281B SER* 5.7 1.1 - - - +
307B PRO 5.5 0.4 - - - -
311B THR* 4.0 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PHE* 4.3 15.0 - - + -
61B MET 3.0 17.4 + - - +
62B PRO 3.9 2.2 - - - +
64B VAL* 1.3 77.0 - - - +
66B ALA* 1.3 67.1 + - - +
69B VAL* 3.0 33.8 + - + +
148B LEU* 3.9 25.6 - - + -
156B VAL* 4.0 20.9 - - + -
159B PHE* 4.6 17.0 - - + -
160B ALA* 3.6 27.1 - - + +
163B LEU* 5.9 0.7 - - + -
189B PHE* 5.0 20.0 - - + -
192B LEU* 5.6 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PRO 2.9 19.4 + - - +
63B ILE 4.4 0.2 - - - +
65B LEU* 1.3 77.0 - - - +
67B SER* 1.3 57.9 + - - +
69B VAL* 3.2 6.3 + - - +
70B VAL* 2.9 33.3 + - - +
189B PHE* 3.7 25.8 - - + +
192B LEU* 3.9 19.3 - - + -
193B ALA* 3.7 19.3 - - + +
196B MET* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 2.9 28.0 + - - -
64B VAL 4.5 0.7 - - - -
66B ALA* 1.3 75.2 - - - +
68B LEU* 1.3 58.5 + - - +
70B VAL* 3.7 3.6 - - - +
71B GLY* 2.9 27.5 + - - -
193B ALA* 3.9 12.8 - - - +
197B TYR* 3.1 25.5 + - - -
303B SER 4.1 3.6 + - - +
307B PRO* 3.0 28.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL* 2.9 43.0 + - + +
65B LEU 3.9 2.0 - - - +
67B SER* 1.3 76.1 - - - +
69B VAL* 1.3 63.4 + - - +
71B GLY* 5.0 0.9 - - - -
72B ALA* 2.9 28.8 + - - +
157B ILE* 4.7 14.4 - - + +
160B ALA* 3.9 16.7 - - + +
161B ILE* 4.8 9.0 - - + +
304B PHE* 3.8 32.5 - - + +
307B PRO* 3.5 35.0 - - + +
308B LEU* 4.3 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 3.0 22.0 + - + +
66B ALA 3.6 7.0 - - - +
68B LEU* 1.3 76.9 - - - +
70B VAL* 1.3 59.7 + - + +
72B ALA 3.5 1.0 - - - -
73B ALA* 2.9 36.9 + - + +
160B ALA* 3.4 31.2 - - + +
163B LEU* 4.4 7.4 - - + -
164B GLY* 4.0 11.8 - - - +
167B ILE* 4.4 13.2 - - + -
186B LEU* 4.8 2.5 - - + -
189B PHE* 3.3 43.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ARG* 6.0 0.4 - - - +
66B ALA 2.9 18.0 + - - +
67B SER* 4.1 4.5 - - - +
69B VAL* 1.3 75.7 - - - +
71B GLY* 1.3 59.9 + - - +
73B ALA 4.0 0.2 - - - -
74B SER* 3.3 27.2 + - - +
186B LEU* 4.3 16.6 - - + +
189B PHE* 3.4 13.7 - - + +
190B ASP* 3.4 54.7 - - + +
193B ALA* 4.6 3.6 - - + -
303B SER* 4.4 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B SER 2.9 12.8 + - - -
68B LEU 3.8 0.4 - - - -
70B VAL* 1.3 79.2 - - - +
72B ALA* 1.3 56.1 + - - +
73B ALA 3.2 3.5 + - - -
74B SER* 3.7 3.2 + - - -
75B ILE* 3.3 28.9 - - - +
299B LYS 5.7 0.2 - - - +
303B SER* 3.4 33.3 + - - -
304B PHE* 3.9 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU 2.9 16.9 + - - +
69B VAL 3.5 2.2 - - - +
71B GLY* 1.3 73.5 - - - +
73B ALA* 1.3 57.0 + - - +
74B SER 3.8 0.2 - - - -
75B ILE 4.7 2.0 - - - -
80B LEU* 3.6 30.0 - - + +
161B ILE* 3.6 35.7 - - + +
164B GLY* 3.0 18.9 - - - +
165B ILE* 3.4 2.4 + - - -
168B THR* 4.4 1.6 - - - +
304B PHE* 4.3 10.4 - - + -
----------------------------------------------------------
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