Contacts of the strand formed by residues 7 - 15 (chain A) in PDB entry 2FOL
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 TYR 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A TYR* 3.6 10.6 - - - +
6A ASP* 1.3 102.4 - - + +
8A LEU* 1.3 60.0 + - - +
9A PHE* 3.3 37.7 - + + -
55A LYS* 4.4 9.6 + - + +
56A THR 3.6 1.6 + - - -
57A ILE* 3.5 19.4 - - + -
58A LYS* 3.1 22.3 + - - -
170A LYS* 4.1 35.8 + - + +
173A MET* 4.7 20.8 - - + +
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Residues in contact with LEU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A TYR* 6.3 0.4 - - + -
7A TYR* 1.3 72.9 - - - +
9A PHE* 1.3 70.6 + - - +
10A LYS* 4.0 14.4 + - - +
47A ILE* 6.2 1.1 - - + -
58A LYS* 3.5 38.4 - - + +
59A LEU 4.3 1.6 - - - +
60A GLN* 4.2 30.7 - - + +
82A HIS* 3.6 15.2 + - - -
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Residues in contact with PHE 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A TYR* 3.3 33.9 - + + -
8A LEU* 1.3 82.4 - - - +
10A LYS* 1.3 60.6 + - - +
11A LEU* 3.7 12.8 + - + +
57A ILE* 3.7 25.1 - - + -
58A LYS 2.8 9.7 + - - -
59A LEU* 3.2 19.2 - - + -
60A GLN 2.9 24.5 + - - -
82A HIS* 3.9 13.0 - + - -
166A ALA* 3.9 17.0 - - + -
169A ILE* 3.8 29.2 - - + -
170A LYS* 3.9 21.5 - - + -
173A MET* 3.6 25.8 - - + -
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Residues in contact with LYS 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.0 16.3 + - + +
9A PHE* 1.3 70.2 - - - +
11A LEU* 1.3 60.6 + - - +
60A GLN* 3.4 25.5 + - + +
62A TRP* 3.3 32.6 - - + -
80A GLY* 3.5 22.2 - - - +
81A ALA* 3.3 6.3 - - - +
82A HIS* 2.8 51.4 + - + -
83A GLY 3.7 1.9 + - - -
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A PHE* 3.8 17.0 - - + +
10A LYS* 1.3 79.9 - - - +
12A LEU* 1.3 62.6 + - - +
13A LEU* 6.1 0.2 - - + -
59A LEU* 4.1 18.8 - - + -
60A GLN 2.8 14.2 + - - +
61A ILE* 4.2 16.6 - - + -
62A TRP* 3.1 28.3 + - - -
81A ALA* 4.9 0.4 - - - -
83A GLY 3.3 7.9 - - - +
85A ILE* 4.9 5.2 - - + -
162A PHE* 3.8 32.3 - - + +
165A MET* 3.9 22.9 - - + -
166A ALA 5.5 0.9 - - - +
169A ILE* 3.8 28.3 - - + -
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Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 1.3 78.7 - - - +
13A LEU* 1.3 64.7 + - - +
14A ILE* 5.3 1.8 - - + -
61A ILE* 5.0 0.2 - - - +
62A TRP* 3.4 32.5 - - + +
63A ASP 5.0 2.0 - - - +
78A TYR* 3.7 55.9 - - + +
81A ALA* 4.2 7.6 - - + -
83A GLY 3.3 3.8 + - - -
84A ILE* 3.2 26.6 - - + +
85A ILE 2.7 32.5 + - - -
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 6.1 0.2 - - + -
12A LEU* 1.3 78.3 - - - +
14A ILE* 1.3 62.0 + - - +
21A LYS* 3.3 54.1 + - + +
24A LEU* 4.7 6.1 - - + -
25A LEU* 4.0 19.1 - - + +
61A ILE* 4.5 7.2 - - + -
62A TRP 3.2 22.1 + - - +
63A ASP* 4.5 12.0 - - + +
85A ILE* 3.4 42.6 - - + +
87A VAL* 4.7 5.8 - - + -
162A PHE* 4.2 13.9 - - + -
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Residues in contact with ILE 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 4.6 3.6 - - + +
13A LEU* 1.3 75.1 - - - +
15A GLY* 1.3 57.9 + - - +
21A LYS* 3.6 11.8 - - - +
78A TYR* 3.9 19.7 - - + +
84A ILE* 3.1 33.9 - - + -
85A ILE 2.8 9.6 + - - +
86A VAL* 3.6 10.1 - - + -
87A VAL* 2.9 24.8 + - - +
102A TRP* 2.9 55.6 - - + +
106A ILE* 3.3 28.3 - - + -
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Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE* 1.3 83.2 - - - +
16A ASP* 1.3 63.3 + - - -
17A SER 3.8 0.3 + - - -
19A VAL* 4.8 0.2 - - - -
21A LYS* 3.0 23.0 + - - +
86A VAL* 5.2 0.2 - - - -
87A VAL 3.4 16.2 - - - -
102A TRP* 3.3 28.6 - - - -
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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