Contacts of the strand formed by residues 1 - 14 (chain B) in PDB entry 3E7H
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 1 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0B ALA* 1.3 90.5 + - + +
2B ASN* 1.3 71.2 + - - +
3B PHE* 4.3 4.3 + - + +
88B GLN* 3.7 37.5 - - + +
89B GLU 3.3 5.6 - - - +
90B ILE* 4.3 20.4 - - + -
95B LEU* 4.8 8.7 - - + -
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Residues in contact with ASN 2 (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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0B ALA 4.2 4.5 - - - +
1B VAL* 1.3 81.2 + - - +
3B PHE* 1.3 61.8 + - - +
4B GLU* 3.8 2.5 - - + +
87B ASN 3.5 1.4 - - - +
88B GLN* 3.5 2.3 - - - -
89B GLU* 2.7 63.2 + - + +
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Residues in contact with PHE 3 (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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3A PHE* 6.3 3.6 - + - -
1B VAL* 4.3 4.0 + - + +
2B ASN* 1.3 74.1 - - - +
4B GLU* 1.3 60.0 + - - +
5B VAL* 3.6 15.0 + - + +
84B ILE* 3.8 29.2 - - + -
86B ALA* 3.3 27.1 - - + -
87B ASN 3.7 2.0 - - - -
88B GLN* 4.0 38.1 - - + -
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Residues in contact with GLU 4 (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 ASN* 3.8 1.7 - - + -
3B PHE* 1.3 70.3 - - - +
5B VAL* 1.3 64.3 + - - +
6B LYS* 3.1 39.3 + - + +
86B ALA* 3.2 3.4 - - - -
87B ASN* 2.9 51.5 + - + +
89B GLU* 3.8 21.9 - - - +
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Residues in contact with VAL 5 (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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3B PHE* 3.6 18.5 + - + +
4B GLU* 1.3 74.9 - - - +
6B LYS* 1.3 65.4 + - - +
7B ASP 3.5 13.7 - - - +
8B GLN* 3.3 28.3 - - + +
84B ILE* 3.8 24.7 - - + -
85B THR 3.6 5.4 - - - +
86B ALA* 4.1 0.9 - - - -
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Residues in contact with LYS 6 (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 GLU* 3.1 48.1 + - - +
5B VAL* 1.3 81.9 - - - +
7B ASP* 1.3 65.6 + - - +
8B GLN* 4.7 1.1 - - - -
85B THR* 2.7 20.4 + - + +
86B ALA* 4.6 1.8 - - - +
87B ASN* 3.4 23.3 - - - +
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Residues in contact with ASP 7 (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 VAL* 3.5 6.2 - - - +
6B LYS* 1.3 80.2 - - + +
8B GLN* 1.3 102.4 + - - +
84B ILE* 3.8 0.5 - - - -
85B THR* 2.9 46.9 + - + +
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Residues in contact with GLN 8 (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 VAL* 3.3 20.7 - - + +
6B LYS 4.7 0.7 - - - -
7B ASP* 1.3 104.7 + - - +
9B THR* 1.3 63.4 + - - +
62B VAL* 3.9 21.9 + - + +
82B LEU* 5.1 4.7 - - + -
83B ILE 3.4 10.3 - - - +
84B ILE* 4.9 5.4 - - + -
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Residues in contact with THR 9 (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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8B GLN* 1.3 76.9 - - - +
10B LEU* 1.3 77.7 + - - +
11B MET* 4.4 2.5 - - + -
59B GLU* 3.6 32.7 + - - +
60B VAL 3.3 9.6 + - - -
61B PRO* 4.9 1.3 - - - +
62B VAL* 3.9 13.5 - - - +
82B LEU* 3.7 3.3 - - - +
83B ILE* 2.8 57.5 + - + +
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Residues in contact with LEU 10 (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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9B THR* 1.3 87.7 + - - +
11B MET* 1.3 70.8 + - - +
12B MET* 3.9 25.1 - - + -
59B GLU* 3.3 0.2 - - - -
60B VAL* 2.9 34.0 + - + +
61B PRO 3.6 17.5 - - - +
62B VAL* 3.9 13.6 - - + +
64B TYR* 4.0 10.8 - - + -
65B ILE* 4.1 28.5 - - + -
81B GLU 3.0 18.4 - - - +
82B LEU* 3.8 26.7 - - + -
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Residues in contact with MET 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR* 4.4 1.8 - - + -
10B LEU* 1.3 78.2 - - - +
12B MET* 1.3 67.1 + - - +
30B ALA* 4.6 10.1 - - + -
31B ASP* 5.3 7.9 - - - +
57B PHE* 3.8 37.2 - - + +
58B ILE* 3.2 16.4 - - - +
59B GLU* 3.9 22.7 - - + +
60B VAL 4.5 0.2 - - - +
79B THR 4.2 0.9 - - - +
80B GLY* 3.4 1.0 - - - -
81B GLU* 2.9 50.2 + - - +
83B ILE* 3.4 21.5 - - + +
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Residues in contact with MET 12 (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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65A ILE 5.9 0.7 - - - +
10B LEU* 3.9 21.1 - - + -
11B MET* 1.3 79.2 - - - +
13B GLU* 1.3 64.7 + - - +
14B LEU 3.5 0.2 + - - -
57B PHE* 3.3 7.1 - - - -
58B ILE* 3.0 34.0 + - - +
60B VAL* 4.1 13.4 - - + +
64B TYR* 3.6 32.5 - - + -
65B ILE* 4.5 8.7 - - + -
75B VAL* 3.9 35.0 - - + -
76B ASN 3.9 11.9 - - - +
77B GLU* 4.1 24.0 - - + +
79B THR* 3.7 4.5 - - - -
80B GLY* 4.0 11.7 - - - -
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Residues in contact with GLU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B MET* 1.3 71.1 - - - +
14B LEU* 1.3 69.8 + - - +
15B VAL* 3.9 1.8 + - + +
56B ASN* 3.3 24.0 - - + +
57B PHE* 3.5 18.5 - - + -
75B VAL* 3.4 5.4 - - - -
76B ASN* 3.0 39.5 + - + +
79B THR* 2.9 38.6 + - + +
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Residues in contact with LEU 14 (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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12B MET 3.5 1.2 + - - -
13B GLU* 1.3 84.0 - - - +
15B VAL* 1.3 67.5 + - - +
16B PRO* 3.4 27.1 - - + +
19B LEU* 3.9 24.5 - - + -
50B LEU* 4.0 26.9 - - + -
55B VAL 3.8 19.3 - - - +
56B ASN* 2.9 22.7 + - - +
58B ILE* 4.0 35.2 - - + -
74B TYR* 3.5 17.3 - - + +
75B VAL* 4.8 1.1 - - - +
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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