Contacts of the strand formed by residues 77 - 83 (chain B) in PDB entry 1F3F
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 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B ALA* 3.8 24.0 - - + -
15B VAL 3.3 13.2 - - - +
16B LYS* 4.2 2.2 - - + -
17B PRO* 3.5 33.7 - - + -
20B VAL* 4.0 0.4 - - - -
43B LYS 3.8 0.5 - - - +
44B GLN* 3.2 3.1 - - - -
45B LEU* 2.8 35.3 + - + +
47B PRO* 3.6 23.1 - - + -
72B ILE* 3.8 6.7 - - + +
76B PRO* 1.3 74.3 - - - +
78B VAL* 1.3 70.8 + - - +
79B ALA 3.8 0.6 + - - +
137B TRP* 4.1 18.8 - - + -
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Residues in contact with VAL 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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14B ALA* 3.4 1.9 - - - -
15B VAL* 2.7 72.8 + - + -
20B VAL* 3.9 3.1 - - + +
25B VAL* 3.8 32.5 - - + -
42B LEU* 5.1 5.8 - - + -
43B LYS 3.4 7.0 - - - +
44B GLN* 3.9 29.2 - - + +
77B VAL* 1.3 78.4 - - - +
79B ALA* 1.3 62.2 + - - +
80B MET* 3.8 9.4 - - + +
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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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12B PHE* 3.7 21.5 - - + -
13B LEU 3.6 4.7 - - - -
14B ALA* 4.4 1.3 - - - +
42B LEU* 3.4 3.8 - - - +
43B LYS* 2.9 37.0 + - + +
45B LEU* 4.0 8.3 - - + -
77B VAL* 3.8 2.2 + - - -
78B VAL* 1.3 70.0 - - - +
80B MET* 1.3 66.4 + - - +
137B TRP* 3.7 23.6 - - + -
138B PHE* 3.5 13.0 - - + -
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Residues in contact with MET 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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12B PHE* 3.5 4.6 - - - -
13B LEU* 2.8 72.0 + - + +
14B ALA 4.6 0.4 - - - +
15B VAL* 4.0 23.3 - - + -
28B ILE* 4.1 13.5 - - + -
29B ILE* 3.8 30.5 - - - -
39B LEU* 4.2 6.7 - - + -
41B GLY 3.3 9.9 - - - +
42B LEU* 3.7 11.9 - - + -
78B VAL* 3.8 7.0 - - + +
79B ALA* 1.3 82.7 - - - +
81B VAL* 1.3 70.0 + - - +
82B PHE* 3.9 14.8 - - + -
121B ILE* 4.6 1.8 - - + -
138B PHE* 4.0 1.1 - - - -
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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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10B ARG* 4.0 10.8 - - + -
11B THR 3.3 13.9 - - - +
12B PHE* 4.4 2.5 - - + -
39B LEU* 3.6 5.0 - - - +
40B VAL* 2.8 47.0 + - + -
41B GLY 2.9 10.9 + - - +
80B MET* 1.3 80.5 - - - +
82B PHE* 1.3 61.8 + - - +
134B ILE* 3.6 35.2 - - + -
138B PHE* 3.4 29.6 - - + -
143B LEU* 3.9 11.7 - - + -
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Residues in contact with PHE 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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10B ARG* 3.3 3.3 - - - -
11B THR* 2.9 34.7 + - + -
13B LEU* 3.7 19.7 - - + -
29B ILE* 4.3 18.2 - - + -
32B TYR* 3.5 33.4 - + + -
33B GLU* 4.4 4.9 - - + -
37B PHE* 3.7 23.8 - - + -
38B VAL 3.2 17.0 - - - -
39B LEU* 3.6 36.3 - - + -
40B VAL* 4.4 1.3 - - - -
80B MET* 3.9 23.1 - - + -
81B VAL* 1.3 75.6 - - - +
83B GLU* 1.3 60.6 + - - +
87B VAL* 3.5 21.1 - - + +
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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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7B ASN 3.9 3.6 - - - +
8B LYS* 3.6 38.9 + - - +
9B GLU 3.1 12.6 - - - +
10B ARG* 2.7 43.8 + - + -
36B GLY 4.7 0.2 - - - +
37B PHE* 3.6 9.0 - - - -
38B VAL* 2.8 35.6 + - + +
40B VAL* 3.7 14.2 - - + +
82B PHE* 1.3 75.1 - - - +
84B GLY* 1.3 61.8 + - - +
87B VAL* 4.3 0.2 - - - -
147B VAL* 3.3 32.3 - - + +
154B TYR* 4.5 0.7 + - - -
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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