Contacts of the helix formed by residues 62 - 76 (chain B) in PDB entry 4I7H
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 62 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B TYR* 3.3 12.3 - - - -
60B ASN 3.6 2.5 + - - -
61B MET* 1.3 79.6 - - - +
63B LEU* 1.3 65.2 + - - +
64B ALA* 3.3 13.7 + - - +
65B THR* 3.1 39.4 + - - -
66B VAL 3.3 4.7 + - - -
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Residues in contact with LEU 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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47B ALA* 3.9 15.9 - - + +
48B ASP* 4.2 13.2 - - + +
51B TYR* 3.3 46.8 - - + -
62B SER* 1.3 72.6 - - - +
64B ALA* 1.3 62.4 + - - +
66B VAL* 3.1 5.4 + - + +
67B TYR* 3.0 58.6 + - + +
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B SER* 3.1 12.4 + - - +
63B LEU* 1.3 78.7 - - - +
65B THR* 1.3 56.2 + - - +
67B TYR* 3.4 6.8 + - - +
68B ASN* 2.8 45.7 + - - +
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Residues in contact with THR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B THR* 3.9 20.2 - - + -
60B ASN 4.1 6.8 + - - -
61B MET* 4.3 7.9 - - + -
62B SER* 3.1 33.3 + - - -
64B ALA* 1.3 75.2 - - - +
66B VAL* 1.3 62.8 + - - +
68B ASN* 3.3 7.1 + - - +
69B ASN* 3.0 46.3 + - - +
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 4.3 10.3 - - + +
47B ALA* 3.7 22.2 - - + +
50B ILE* 3.9 18.8 - - + -
51B TYR* 3.7 29.8 - - + +
61B MET* 3.9 17.9 - - + -
62B SER 3.8 9.9 - - - +
63B LEU* 3.1 10.6 + - + +
65B THR* 1.3 77.6 - - - +
67B TYR* 1.3 63.3 + - - +
69B ASN* 3.3 1.9 + - - +
70B LEU* 3.0 42.2 + - + +
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Residues in contact with TYR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 3.3 19.9 + - + +
48B ASP* 5.0 2.1 + - - +
63B LEU* 3.0 58.6 + - + +
64B ALA* 3.9 7.9 - - - +
66B VAL* 1.3 75.8 - - - +
68B ASN* 1.3 65.0 + - - +
70B LEU* 3.3 6.3 + - + +
71B LYS* 2.9 23.6 + - - +
89B THR* 5.8 3.6 - - - +
90B THR* 5.4 7.8 + - + +
92B TYR* 3.5 27.8 - + - -
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Residues in contact with ASN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ARG* 5.1 0.9 - - - -
64B ALA* 2.8 35.2 + - - +
65B THR* 3.8 7.3 - - - +
66B VAL 3.3 0.2 - - - -
67B TYR* 1.3 75.9 - - - +
69B ASN* 1.3 64.5 + - - +
71B LYS* 3.3 8.3 + - - +
72B VAL* 3.3 25.4 + - - +
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Residues in contact with ASN 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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28B THR* 4.7 2.5 + - - -
30B THR* 4.1 5.5 - - - +
31B ARG* 2.6 52.9 + - - +
34B ILE* 3.7 28.8 - - + +
65B THR* 3.0 44.2 + - - +
66B VAL 3.8 0.4 - - - +
68B ASN* 1.3 74.9 - - - +
70B LEU* 1.3 66.3 + - - +
72B VAL* 3.1 4.5 + - - +
73B LEU* 3.0 29.6 + - + +
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Residues in contact with LEU 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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34B ILE* 4.5 14.6 - - + -
38B MET* 4.4 8.7 - - + -
47B ALA* 4.0 7.4 - - + -
50B ILE* 4.0 19.1 - - + -
66B VAL* 3.0 40.5 + - + +
67B TYR* 3.6 6.7 - - - +
69B ASN* 1.3 76.6 - - - +
71B LYS* 1.3 58.4 + - - +
73B LEU* 3.2 8.9 + - + +
74B VAL* 2.8 35.7 + - - +
79B VAL* 4.5 7.5 - - + +
92B TYR* 3.7 59.0 - - + +
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR 2.9 13.9 + - - +
68B ASN* 3.6 12.1 - - - +
69B ASN 3.2 0.4 - - - -
70B LEU* 1.3 76.9 - - - +
72B VAL* 1.3 58.4 + - + +
74B VAL* 3.4 9.0 + - - +
75B ASP* 2.9 59.0 + - - +
81B GLU* 2.8 36.3 + - - +
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Residues in contact with VAL 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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20B LEU* 5.3 3.4 - - + -
25B ILE* 4.4 12.3 - - + -
31B ARG* 3.5 37.0 - - - +
68B ASN 3.3 13.0 + - - +
69B ASN 3.1 7.5 + - - +
71B LYS* 1.3 75.8 - - + +
73B LEU* 1.3 62.4 + - + +
75B ASP* 3.3 6.8 + - - +
76B GLU* 2.9 43.3 + - + +
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Residues in contact with LEU 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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16B VAL* 4.4 14.1 - - + -
20B LEU* 4.5 12.6 - - + -
31B ARG* 5.0 11.0 - - + -
34B ILE* 4.4 20.6 - - + -
35B ILE* 3.9 38.6 - - + -
38B MET* 5.6 0.9 - - + -
69B ASN* 3.0 19.7 + - + +
70B LEU* 3.7 8.7 - - + +
72B VAL* 1.3 77.2 - - + +
74B VAL* 1.3 62.3 + - - +
76B GLU* 3.6 2.8 + - - -
77B GLY 3.1 3.8 + - - -
78B PHE* 2.8 37.2 + - + -
79B VAL* 3.3 28.0 + - + -
94B PHE* 5.5 2.0 - - + -
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Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU 2.8 25.5 + - - +
71B LYS* 3.6 15.7 - - - +
73B LEU* 1.3 71.9 - - - +
75B ASP* 1.3 60.5 + - - +
77B GLY* 2.8 25.5 + - - -
79B VAL* 3.4 33.5 - - + +
80B SER* 5.5 0.2 - - - -
81B GLU* 3.5 45.1 - - + +
92B TYR* 4.6 2.5 - - + -
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Residues in contact with ASP 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS* 2.9 49.4 + - - +
72B VAL* 3.3 6.7 + - - +
74B VAL* 1.3 76.2 - - - +
76B GLU* 1.3 66.9 + - - +
77B GLY* 3.2 0.7 + - - -
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Residues in contact with GLU 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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20B LEU* 4.2 8.2 - - + +
23B LYS* 3.4 30.5 - - - +
25B ILE* 3.4 33.0 - - + +
72B VAL* 2.9 27.9 + - + +
73B LEU* 4.2 2.0 - - - +
74B VAL 3.2 0.2 - - - -
75B ASP* 1.3 82.5 - - + +
77B GLY* 1.3 60.9 + - - +
78B PHE* 3.3 31.3 - - + -
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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