Contacts of the helix formed by residues 65 - 76 (chain B) in PDB entry 10GS
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 65 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 3.3 46.3 + - - -
17B LEU* 4.7 3.4 - - - +
53B PRO* 4.2 6.0 - - - +
64B GLN* 1.3 69.7 - - - +
66B ASN* 1.3 60.5 + - - +
68B ILE* 3.2 16.5 + - - +
69B LEU* 2.9 33.1 + - - +
210B VWW 2.7 33.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ASP* 3.7 15.0 + - - +
13B ARG* 4.2 1.4 - - - +
64B GLN* 3.3 1.2 - - - +
65B SER* 1.3 84.2 + - - +
67B THR* 1.3 60.0 + - - +
69B LEU* 3.3 9.3 + - - +
70B ARG* 2.9 49.5 + - - +
93B ASN* 2.9 24.0 + - - +
97B GLU* 2.9 38.3 + - - +
154B ASN* 3.7 14.7 + - - -
210B VWW 4.5 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA* 3.2 28.9 - - - +
90A ASP* 3.2 12.2 - - + -
91A MET* 3.2 25.8 + - + +
94A ASP* 2.8 22.2 + - - -
62B LEU* 4.1 14.4 - - + -
63B TYR 3.4 12.6 - - - +
64B GLN* 3.0 11.7 + - - +
66B ASN* 1.3 74.6 - - - +
68B ILE* 1.3 57.7 + - - +
70B ARG* 3.3 3.3 + - - +
71B HIS* 2.8 28.4 + - - +
74B ARG* 4.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 4.0 18.2 - - + -
53B PRO* 4.0 22.7 - - + +
55B PHE* 3.7 51.1 - - + +
62B LEU* 4.3 13.7 - - + -
63B TYR 4.4 5.4 - - - +
64B GLN 3.1 19.4 + - - +
65B SER* 3.2 15.7 + - - +
67B THR* 1.3 75.9 - - - +
69B LEU* 1.3 61.8 + - - +
71B HIS* 3.2 7.1 + - - +
72B LEU* 3.0 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ALA* 4.3 9.4 - - + +
17B LEU* 3.9 35.4 - - + +
20B LEU* 4.0 18.8 - - + -
65B SER* 2.9 17.1 + - - +
66B ASN* 3.6 18.6 - - - +
67B THR 3.3 0.2 - - - -
68B ILE* 1.3 76.3 - - - +
70B ARG* 1.3 57.8 + - - +
72B LEU* 3.3 5.0 + - + +
73B GLY* 2.8 26.5 + - - -
93B ASN* 4.3 4.3 - - - +
150B PHE* 3.8 27.0 - - + +
153B TYR* 5.5 0.2 - - + -
154B ASN* 3.7 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 3.6 41.6 - - - +
90A ASP* 3.7 21.5 - - - +
94A ASP* 4.5 2.2 + - - -
66B ASN* 2.9 41.7 + - - +
67B THR 3.8 2.0 - - - +
69B LEU* 1.3 75.5 - - - +
71B HIS* 1.3 57.3 + - - +
73B GLY 3.4 0.5 + - - -
74B ARG* 2.9 33.3 + - - +
79B TYR* 3.3 21.6 + - + +
90B ASP* 2.8 39.0 + - - +
93B ASN* 4.0 15.1 - - - +
94B ASP* 3.1 25.7 + - - -
150B PHE* 3.6 18.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLN* 4.6 11.0 + - + +
84A GLN* 5.6 0.4 - - - -
87A ALA* 3.8 18.1 - - + +
55B PHE* 4.4 7.2 - + - -
57B ASP* 2.9 30.6 + - - +
60B LEU* 3.9 17.2 - - + +
62B LEU* 3.8 24.7 - - + -
67B THR 2.8 18.1 + - - +
68B ILE 3.5 3.8 - - - +
70B ARG* 1.3 77.2 - - - +
72B LEU* 1.3 72.9 + - + +
74B ARG* 3.3 12.4 + - - +
75B THR* 2.9 54.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TYR* 4.2 17.0 - - + +
17B LEU* 4.6 11.9 - - + -
20B LEU* 4.2 21.8 - - + -
21B LEU* 4.3 25.6 - - + -
55B PHE* 3.9 23.3 - - + -
68B ILE* 3.0 33.7 + - + +
69B LEU* 3.7 4.9 - - - +
71B HIS* 1.3 92.6 - - + +
73B GLY* 1.3 61.6 + - - +
75B THR* 3.6 6.5 - - - +
76B LEU* 2.8 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 5.1 0.2 - - - +
69B LEU 2.8 16.7 + - - -
70B ARG 3.8 1.8 - - - -
72B LEU* 1.3 77.1 - - - +
74B ARG* 1.3 58.3 + - - +
77B GLY* 3.1 7.4 + - - -
78B LEU* 2.7 51.5 + - - -
79B TYR* 3.6 9.6 + - - +
150B PHE* 4.1 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ARG* 5.7 0.4 - - - +
79A TYR* 3.7 20.6 + - - -
83A GLN* 3.4 31.3 + - + +
86A ALA* 3.7 21.2 - - - +
87A ALA* 3.7 23.4 - - - +
90A ASP* 3.1 28.5 + - - -
67B THR 4.9 0.2 + - - -
70B ARG* 2.9 15.4 + - - +
71B HIS* 3.6 24.0 + - - +
73B GLY* 1.3 79.6 - - - +
75B THR* 1.3 62.6 + - + +
76B LEU 3.6 0.2 + - - -
77B GLY* 3.7 6.6 + - - -
79B TYR* 3.8 29.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLN* 3.4 32.1 - - + +
3B TYR* 4.8 3.3 + - - -
57B ASP* 5.0 4.1 + - - +
71B HIS* 2.9 45.4 + - + +
72B LEU* 3.4 13.3 + - - +
74B ARG* 1.3 75.8 - - + +
76B LEU* 1.3 75.1 + - - +
77B GLY 3.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TYR* 3.8 20.9 - - - +
20B LEU* 4.0 24.9 - - + -
21B LEU* 4.9 1.6 - - + -
24B GLN* 4.5 12.6 - - + +
26B GLN* 4.2 32.5 - - + +
72B LEU* 2.8 31.2 + - + +
75B THR* 1.3 86.3 - - - +
77B GLY* 1.3 62.5 + - - +
78B LEU* 4.1 16.4 - - + +
----------------------------------------------------------
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