Contacts of the helix formed by residues 75 - 90 (chain B) in PDB entry 1C03
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 LEU 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B ILE 3.8 6.3 - - - +
9B ILE* 4.3 18.6 - - + -
35B PHE* 3.4 39.7 - - + -
70B SER* 2.8 24.3 + - - +
71B ALA* 4.8 0.4 - - - +
73B LEU* 4.1 21.3 - - + +
74B GLY* 1.3 77.6 - - - +
76B GLN* 1.3 61.1 + - - +
77B ARG 3.4 3.0 + - - -
78B ILE* 3.4 18.1 + - + +
79B ALA* 3.3 17.7 + - - +
155B ALA* 4.2 15.7 - - + -
159B LEU* 4.1 27.4 - - + -
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Residues in contact with GLN 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PRO* 3.6 30.1 - - + +
7B GLU* 2.7 48.8 + - - +
8B ILE 3.5 4.8 + - - +
9B ILE 4.0 4.4 + - - -
10B ASN* 3.7 27.8 - - + +
71B ALA* 5.8 1.6 - - - +
74B GLY* 3.1 7.6 + - - +
75B LEU* 1.3 71.9 - - - +
77B ARG* 1.3 60.8 + - - +
79B ALA* 3.8 9.9 - - - +
80B TRP* 3.2 23.9 + - - +
20D MET* 6.5 0.4 - - - -
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Residues in contact with ARG 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 3.7 18.5 - - + +
5B PRO* 2.8 27.9 + - + +
6B SER 4.1 1.2 + - - -
7B GLU 3.6 17.7 - - - +
8B ILE* 4.0 19.0 + - + +
75B LEU 3.4 0.8 - - - -
76B GLN* 1.3 76.0 - - - +
78B ILE* 1.3 65.9 + - + +
80B TRP* 3.6 5.4 + - - +
81B VAL* 3.2 28.3 + - - +
102B LEU 3.0 14.6 + - - -
103B VAL* 5.2 0.6 - - - +
105B THR* 2.5 32.3 + - - -
106B LEU* 3.6 37.8 - - - +
151B GLU* 2.6 61.5 + - + +
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PHE* 4.0 27.1 - - + -
43B PHE* 5.1 11.7 - - + -
66B LEU* 4.7 5.8 - - + -
70B SER* 4.0 14.1 - - - +
75B LEU* 3.4 16.1 + - + +
77B ARG* 1.3 79.8 - - + +
79B ALA* 1.3 61.1 + - - +
81B VAL* 3.3 5.2 + - - +
82B CYS* 3.1 32.9 + - - -
148B SER* 5.1 5.4 - - - +
151B GLU* 3.9 24.5 - - + +
152B PHE* 3.8 25.6 - - + +
155B ALA* 4.0 15.9 - - + -
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LYS* 4.0 16.4 - - - +
70B SER* 3.6 18.6 + - - +
71B ALA* 4.3 12.1 - - + +
75B LEU 3.3 12.4 + - - +
76B GLN* 3.9 9.9 - - - +
77B ARG 3.2 0.4 - - - -
78B ILE* 1.3 79.6 - - - +
80B TRP* 1.3 56.6 + - - +
82B CYS* 3.2 7.5 + - - +
83B GLU* 2.9 28.0 + - - +
20D MET* 4.4 15.0 - - + -
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Residues in contact with TRP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B SER* 3.4 33.2 - - - -
3B THR* 3.8 12.2 + - - -
4B ILE* 3.5 52.4 - - + +
5B PRO* 4.0 14.1 - - + -
76B GLN 3.2 16.1 + - - +
77B ARG* 3.7 4.3 - - - +
79B ALA* 1.3 78.0 - - - +
81B VAL* 1.3 71.1 + - + +
83B GLU* 3.2 14.9 + - - +
84B ARG* 3.1 67.9 + - + +
96B PHE* 4.0 19.7 - + - -
97B PRO* 4.8 3.1 - - + -
102B LEU* 4.3 11.2 - - + -
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 4.4 2.5 - - + -
77B ARG 3.2 16.9 + - - +
78B ILE* 3.3 4.9 + - - +
80B TRP* 1.3 94.1 - - + +
82B CYS* 1.3 59.4 + - - +
84B ARG* 3.1 5.4 + - - +
85B ILE* 2.9 26.4 + - + +
96B PHE* 4.1 14.1 - - + -
144B ALA* 3.2 22.2 - - + +
147B GLN* 4.1 17.7 - - + -
148B SER* 3.1 27.4 - - - +
151B GLU* 4.2 11.0 - - + -
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Residues in contact with CYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B PHE* 5.6 0.2 - - - -
46B MET* 5.2 1.1 - - - -
63B GLY* 3.5 22.0 - - - +
66B LEU* 3.7 42.4 - - - -
67B LYS* 3.8 8.1 - - + -
78B ILE* 3.1 23.5 + - - +
79B ALA 3.5 8.1 - - - +
81B VAL* 1.3 76.9 - - - +
83B GLU* 1.3 57.9 + - - +
85B ILE* 3.2 14.2 + - - +
86B GLN* 3.0 31.9 + - - +
148B SER* 4.7 7.6 - - - -
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LYS* 3.0 33.4 + - - +
79B ALA 2.9 13.1 + - - +
80B TRP* 3.2 16.5 - - - +
82B CYS* 1.3 78.0 - - - +
84B ARG* 1.3 85.6 + - - +
86B GLN* 3.5 13.2 + - - +
87B ASN* 3.1 28.0 + - - +
20D MET* 3.8 16.4 - - - +
23D ASP* 3.3 32.5 - - + +
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Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B SER* 5.9 0.7 - - - -
80B TRP* 3.1 75.8 + - + +
81B VAL 3.1 6.3 + - - +
83B GLU* 1.3 97.3 + - - +
85B ILE* 1.3 62.4 + - - +
86B GLN 3.1 0.2 - - - -
87B ASN* 3.4 7.9 + - - +
88B LEU* 2.8 40.2 + - + +
93B GLU* 2.8 44.1 + - - +
95B PHE 6.0 1.3 - - - +
96B PHE* 3.9 23.3 - - + -
97B PRO* 6.2 0.4 - - - -
144B ALA* 5.2 0.2 - - + -
23D ASP* 2.9 22.0 + - - -
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B MET* 4.3 26.5 - - + -
59B LEU* 3.4 26.5 - - + +
63B GLY* 4.5 6.1 - - - -
81B VAL 2.9 17.0 + - - +
82B CYS* 3.2 13.7 + - - +
84B ARG* 1.3 75.2 - - - +
86B GLN* 1.3 61.9 + - - +
88B LEU* 3.8 8.1 - - - +
89B GLY* 3.0 19.2 + - - -
141B ILE* 4.1 24.9 - - + +
144B ALA* 3.6 26.5 - - + -
145B LEU* 4.3 6.3 - - + +
148B SER* 4.0 20.9 - - - +
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Residues in contact with GLN 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ASP* 3.1 32.6 - - - +
63B GLY* 3.9 7.2 - - - -
64B HIS* 3.2 27.8 + - - +
67B LYS* 3.3 26.3 - - - +
82B CYS 3.0 14.3 + - - +
83B GLU* 3.5 11.5 - - - +
84B ARG 3.1 0.2 - - - -
85B ILE* 1.3 73.8 - - - +
87B ASN* 1.3 64.1 + - - +
89B GLY* 2.9 17.3 + - - -
90B ARG* 3.0 42.8 + - - +
24D ASP* 2.7 26.4 + - - +
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Residues in contact with ASN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLU* 3.1 14.3 + - - +
84B ARG* 3.4 10.0 + - - +
86B GLN* 1.3 78.0 - - - +
88B LEU* 1.3 62.1 + - - +
90B ARG* 3.1 23.4 + - - +
91B LYS 3.0 4.2 + - - -
92B MET* 3.0 34.3 + - + +
93B GLU* 2.8 47.4 - - + +
23D ASP* 3.7 28.9 + - - +
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ARG* 2.8 32.4 + - + +
85B ILE 3.8 3.6 - - - +
87B ASN* 1.3 72.6 - - - +
89B GLY* 1.3 62.9 + - - +
91B LYS* 3.2 9.2 + - - +
93B GLU* 3.5 30.5 - - + +
95B PHE 3.9 18.4 - - - +
96B PHE* 4.4 13.2 - - + -
137B TYR* 3.4 27.3 - - + +
140B LEU* 3.4 50.5 - - + +
141B ILE* 3.8 15.7 - - + +
144B ALA* 4.5 5.6 - - + -
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Residues in contact with GLY 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 3.4 44.8 - - - +
60B ASP* 5.0 3.0 - - - +
85B ILE 3.0 11.8 + - - -
86B GLN* 2.9 9.5 + - - -
88B LEU* 1.3 76.0 - - - +
90B ARG* 1.3 58.6 + - - +
91B LYS* 3.4 1.7 - - - +
141B ILE* 4.0 12.8 - - - +
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Residues in contact with ARG 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ASP* 2.8 33.1 + - - +
64B HIS* 5.8 0.2 + - - -
86B GLN* 3.0 39.3 + - - +
87B ASN* 3.1 27.4 + - - +
89B GLY* 1.3 77.7 - - - +
91B LYS* 1.3 72.4 + - - +
92B MET* 3.1 22.1 + - + +
23D ASP 4.1 5.1 + - - -
24D ASP* 3.3 26.9 + - - +
25D SER 5.5 0.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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