Contacts of the helix formed by residues 59 - 75 (chain B) in PDB entry 6P1A
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 ASN 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B TRP* 3.6 2.5 + - - -
58B CYS* 1.3 82.1 - - - +
60B ASP* 1.3 62.6 + - - +
61B ASP* 3.2 9.7 + - - +
62B ASP* 2.7 51.7 + - - -
63B GLY* 3.0 21.3 + - - -
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Residues in contact with ASP 60 (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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26B TRP* 3.1 18.5 + - + +
31B ARG* 2.9 45.9 + - - -
58B CYS 5.1 0.2 - - - +
59B ASN* 1.3 76.8 - - - +
61B ASP* 1.3 66.8 + - - +
64B MET* 2.9 42.6 + - + +
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Residues in contact with ASP 61 (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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59B ASN* 3.2 9.7 + - - +
60B ASP* 1.3 83.0 - - - +
62B ASP* 1.3 66.0 + - - +
64B MET* 3.3 14.3 + - - +
65B LEU* 3.0 23.0 + - - +
152B ARG* 4.1 15.6 + - - +
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Residues in contact with ASP 62 (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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19B TRP* 3.6 30.1 - - + -
58B CYS* 4.1 14.6 - - + +
59B ASN* 2.7 33.5 + - - +
61B ASP* 1.3 72.3 - - - +
63B GLY* 1.3 63.4 + - - +
65B LEU* 3.3 3.8 + - - +
66B ILE* 2.9 31.8 + - + +
149B PHE* 4.5 5.8 - - + -
152B ARG* 2.5 42.2 + - - +
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Residues in contact with GLY 63 (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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23B TRP* 3.8 5.4 - - - -
26B TRP* 3.4 25.7 - - - -
58B CYS* 3.7 10.3 - - - -
59B ASN 3.0 20.3 + - - -
60B ASP 3.7 0.9 - - - -
61B ASP 3.2 0.2 - - - -
62B ASP* 1.3 77.4 - - - +
64B MET* 1.3 56.6 + - - +
66B ILE 3.4 0.2 + - - -
67B SER* 2.8 32.4 + - - -
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Residues in contact with MET 64 (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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26B TRP* 3.7 13.7 - - + -
31B ARG 5.8 0.4 - - - +
32B LEU* 4.9 6.5 - - + -
33B GLU* 5.3 12.3 - - - +
35B ARG* 5.8 0.7 - - - -
36B MET* 4.1 23.7 - - + +
60B ASP* 2.9 31.9 + - + +
61B ASP* 3.8 13.5 - - - +
63B GLY* 1.3 75.3 - - - +
65B LEU* 1.3 56.9 + - - +
67B SER* 3.6 6.5 - - - -
68B GLN* 2.9 45.9 + - - +
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Residues in contact with LEU 65 (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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61B ASP 3.0 16.7 + - - +
62B ASP* 3.6 6.3 - - - +
64B MET* 1.3 77.9 - - - +
66B ILE* 1.3 64.4 + - - +
68B GLN* 3.3 10.0 + - - +
69B VAL* 3.0 27.8 + - + +
145B LEU* 3.6 20.9 - - + -
148B ALA* 3.6 38.8 - - + +
149B PHE* 4.0 19.7 - - + -
152B ARG* 3.7 37.2 - - + +
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Residues in contact with ILE 66 (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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19B TRP* 3.7 41.3 - - + +
20B LEU* 4.3 9.2 - - + -
23B TRP* 3.3 47.3 - - + -
58B CYS* 4.8 3.1 - - - -
62B ASP 2.9 23.0 + - - +
65B LEU* 1.3 77.1 - - - +
67B SER* 1.3 56.3 + - - +
69B VAL* 3.3 5.2 + - + +
70B VAL* 2.9 39.2 + - + +
145B LEU* 4.0 22.9 - - + -
149B PHE* 4.3 5.6 - - + -
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Residues in contact with SER 67 (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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23B TRP* 3.0 22.9 + - - +
26B TRP* 3.2 14.0 - - - -
32B LEU* 3.5 28.9 - - - +
36B MET* 5.3 6.1 - - - -
37B SER* 6.1 0.9 - - - -
40B ILE* 4.9 5.3 - - - +
63B GLY 2.8 23.1 + - - -
64B MET* 3.6 5.4 - - - -
66B ILE* 1.3 77.2 - - - +
68B GLN* 1.3 56.6 + - - +
70B VAL* 3.9 1.8 - - - +
71B ASP* 2.9 32.7 + - - +
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Residues in contact with GLN 68 (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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36B MET* 4.0 37.3 - - - +
64B MET* 2.9 29.5 + - - +
65B LEU* 3.6 8.1 - - - +
67B SER* 1.3 76.1 - - - +
69B VAL* 1.3 63.6 + - + +
71B ASP* 3.9 4.4 - - - +
72B SER* 2.9 26.9 + - - -
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Residues in contact with VAL 69 (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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65B LEU* 3.0 27.4 + - + +
66B ILE* 3.7 6.7 - - + +
68B GLN* 1.3 77.3 - - + +
70B VAL* 1.3 64.6 + - + +
72B SER* 2.9 21.7 + - - -
73B VAL* 3.0 16.8 + - + +
141B ILE* 4.4 9.6 - - + +
144B VAL* 3.5 26.9 - - + -
145B LEU* 3.7 25.1 - - + +
148B ALA* 3.7 29.8 - - + -
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Residues in contact with VAL 70 (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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20B LEU* 4.1 18.8 - - + -
23B TRP* 4.0 15.5 - - + -
66B ILE* 2.9 39.2 + - + +
67B SER 4.1 2.2 - - - +
69B VAL* 1.3 74.7 - - + +
71B ASP* 1.3 58.5 + - - +
73B VAL* 4.6 3.8 - - - -
74B MET* 2.9 33.7 + - + +
81B PHE* 3.9 19.7 - - + -
84B LEU* 3.8 25.6 - - + -
141B ILE* 4.2 15.5 - - + -
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Residues in contact with ASP 71 (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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36B MET 3.9 10.2 - - - +
37B SER* 2.6 40.1 + - - +
38B SER 4.7 0.7 + - - -
39B VAL* 5.2 3.1 + - - +
67B SER 2.9 18.7 + - - +
68B GLN* 3.9 4.0 - - - +
70B VAL* 1.3 78.6 - - - +
72B SER* 1.3 63.3 + - - +
75B TYR* 3.0 38.0 + - - +
81B PHE* 3.9 15.9 - - + -
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Residues in contact with SER 72 (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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68B GLN 2.9 16.2 + - - -
69B VAL* 2.9 18.4 + - - -
71B ASP* 1.3 78.5 + - - +
73B VAL* 1.3 62.0 + - - +
75B TYR* 3.1 26.5 - - - -
144B VAL* 4.3 7.1 - - - +
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Residues in contact with VAL 73 (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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69B VAL* 3.0 20.4 + - + +
70B VAL 4.0 2.2 - - - +
71B ASP 3.2 0.2 - - - -
72B SER* 1.3 85.2 - - - +
74B MET* 1.3 64.9 + - - +
75B TYR* 3.6 2.2 - - - -
76B ILE* 4.0 13.9 - - - +
140B MET* 3.9 33.6 - - + +
141B ILE* 3.7 26.2 - - + -
144B VAL* 3.7 33.7 - - + -
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Residues in contact with MET 74 (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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70B VAL* 2.9 31.4 + - + +
73B VAL* 1.3 90.5 - - + +
75B TYR* 1.3 62.6 + - - +
76B ILE* 3.0 9.1 + - - -
77B ASP* 3.5 20.0 + - + +
78B LYS* 4.5 0.3 + - - -
80B ALA* 3.6 37.0 - - + +
81B PHE* 3.3 30.3 - - + +
84B LEU* 4.3 6.3 - - + -
137B SER* 3.3 38.8 - - - +
140B MET* 4.4 8.3 - - + -
141B ILE* 4.1 11.7 - - + -
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Residues in contact with TYR 75 (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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39B VAL* 5.4 1.6 - - + -
71B ASP* 3.0 25.7 + - - +
72B SER* 3.1 31.0 - - - -
73B VAL 4.4 2.9 - - - -
74B MET* 1.3 76.1 - - - +
76B ILE* 1.3 78.7 + - + +
78B LYS* 3.2 29.4 - - - +
81B PHE* 4.5 7.4 - - - -
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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