Contacts of the strand formed by residues 4 - 12 (chain A) in PDB entry 2FIU
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 GLY 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A LYS* 1.3 73.9 - - - +
5A TYR* 1.3 61.1 + - - -
6A TRP 3.8 0.8 + - - -
57A ILE 3.5 2.4 - - - +
58A GLU* 3.6 1.9 - - - -
59A PHE* 2.8 38.3 + - - +
61A SER 3.5 10.1 - - - -
62A VAL* 3.7 23.1 - - - -
91A ILE* 4.2 4.5 - - - -
92A VAL 3.9 4.0 - - - -
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Residues in contact with TYR 5 (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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3A LYS* 3.7 21.1 - - + +
4A GLY* 1.3 69.8 - - - -
6A TRP* 1.3 63.0 + - - +
7A ILE* 3.5 19.5 + - + +
37A LEU* 3.9 15.3 - - + -
56A VAL* 4.5 9.0 - - + -
57A ILE 3.4 3.1 - - - +
58A GLU* 3.0 50.5 + - + -
90A MSE 3.6 0.3 - - - +
91A ILE* 3.2 5.0 - - - +
92A VAL* 2.8 49.6 + - + +
94A GLY* 3.6 17.0 - - - -
37B LEU* 3.6 47.9 + - + +
38B ALA* 4.3 7.6 - - + -
56B VAL* 4.9 6.3 - - + -
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Residues in contact with TRP 6 (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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4A GLY 3.8 2.6 + - - -
5A TYR* 1.3 69.9 - - - +
7A ILE* 1.3 69.8 + - - +
8A ALA* 4.1 11.3 - - + +
21A TYR* 4.9 1.6 + - - -
29A PHE* 3.7 20.1 - + - -
55A VAL* 5.1 0.9 - - + +
56A VAL* 3.5 3.3 - - - -
57A ILE* 2.8 54.9 + - + +
59A PHE* 3.6 32.5 - + + -
65A ALA* 3.5 26.2 - - + -
68A CYS* 4.1 8.1 - - + -
69A TYR* 3.7 28.9 - + + -
74A TYR* 3.5 29.2 - + - -
89A MSE 3.3 32.0 - - + +
90A MSE 3.4 8.7 - - - -
91A ILE* 4.3 7.0 - - + +
46B LEU* 4.5 8.3 - - + -
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Residues in contact with ILE 7 (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* 3.7 13.2 - - + +
6A TRP* 1.3 78.5 - - - +
8A ALA* 1.3 62.2 + - - +
9A GLN* 4.4 17.1 - - + +
54A ASN* 6.3 0.9 - - + -
55A VAL 3.3 8.5 - - - +
56A VAL* 4.7 16.2 - - + -
88A GLU 3.9 0.9 - - - +
89A MSE 3.3 3.8 - - - -
90A MSE 2.8 60.7 + - + +
92A VAL* 4.1 21.1 - - + -
7B ILE* 4.7 18.2 - - + -
54B ASN* 5.6 0.9 - - + -
56B VAL* 3.5 32.1 - - + -
90B MSE 5.3 0.9 - - + -
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Residues in contact with ALA 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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6A TRP* 4.1 14.8 - - - +
7A ILE* 1.3 74.4 - - - +
9A GLN* 1.3 63.7 + - - +
10A VAL* 4.1 12.3 - - + -
21A TYR* 6.1 1.1 - - - +
53A ARG 3.8 0.5 - - - +
54A ASN* 3.3 4.9 - - - +
55A VAL* 2.9 48.1 + - + +
88A GLU 3.5 4.5 - - - -
89A MSE 3.6 20.9 - - + -
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Residues in contact with GLN 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 ILE* 4.4 10.6 - - + +
8A ALA* 1.3 77.9 - - - +
10A VAL* 1.3 59.0 + - - +
49A THR 5.9 0.8 + - - -
50A ALA* 5.7 2.2 - - - +
51A ARG* 3.5 22.0 - - + +
53A ARG 3.5 4.7 - - - -
54A ASN* 3.6 15.1 + - - +
87A ALA* 3.1 5.0 - - - -
88A GLU* 2.8 55.0 + - - +
90A MSE 4.1 9.2 - - - +
9B GLN* 3.0 41.8 + - - +
88B GLU* 6.1 0.2 - - - +
90B MSE 4.0 17.7 - - + +
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Residues in contact with VAL 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 ALA* 4.2 13.9 - - + +
9A GLN* 1.3 85.2 - - - +
11A ASP* 1.3 61.8 + - - +
12A VAL* 3.8 6.6 + - + -
18A TYR* 3.7 31.4 - - + +
51A ARG* 3.6 7.3 - - - +
52A ALA 3.6 2.3 + - - -
53A ARG* 2.7 53.0 + - + +
55A VAL* 5.2 2.2 - - + -
81A ARG* 4.9 4.3 - - - -
85A ALA* 3.6 27.4 - - + -
86A ASP 3.4 5.8 - - - +
87A ALA* 4.1 12.8 - - + -
89A MSE 5.6 0.4 - - + -
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Residues in contact with ASP 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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10A VAL* 1.3 71.7 - - - +
12A VAL* 1.3 62.3 + - - +
13A ARG* 3.8 2.1 + - - +
50A ALA 5.0 0.2 - - - +
51A ARG* 2.8 44.4 + - - +
52A ALA* 2.9 30.7 + - - +
85A ALA* 3.3 4.0 - - - +
86A ASP* 2.9 34.2 + - + +
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Residues in contact with VAL 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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10A VAL* 3.8 14.8 + - + +
11A ASP* 1.3 75.4 - - - +
13A ARG* 1.3 63.0 + - - +
14A ASP 3.7 17.5 - - - +
15A SER* 3.7 10.1 - - - +
18A TYR* 3.6 54.5 - - + -
52A ALA* 5.9 1.2 - - - +
53A ARG* 4.4 12.3 - - + -
84A VAL 4.4 1.1 - - - +
85A ALA* 4.0 3.6 - - - -
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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