Contacts of the strand formed by residues 85 - 93 (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 ALA 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A VAL* 3.6 21.5 - - + -
11A ASP 3.3 14.8 - - - +
12A VAL* 4.0 6.1 - - - -
13A ARG* 3.7 6.2 + - - +
18A TYR* 4.2 12.6 - - + -
81A ARG* 2.9 19.5 + - + +
82A GLN* 3.9 13.0 - - - +
83A GLU 3.7 1.4 - - - -
84A VAL* 1.3 81.4 - - - +
86A ASP* 1.3 67.1 + - - +
87A ALA* 4.1 2.2 + - - +
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Residues in contact with ASP 86 (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* 3.4 2.8 - - - +
11A ASP* 2.9 37.2 + - + +
13A ARG* 3.0 25.5 + - - +
51A ARG* 3.8 29.0 + - - +
85A ALA* 1.3 74.6 - - - +
87A ALA* 1.3 62.2 + - - +
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Residues in contact with ALA 87 (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 GLN 3.1 11.7 - - - +
10A VAL* 4.1 19.1 - - + -
51A ARG* 4.4 2.1 - - - +
81A ARG* 4.2 24.5 - - + +
85A ALA 4.1 2.4 + - - +
86A ASP* 1.3 75.8 - - - +
88A GLU* 1.3 72.1 + - - +
89A MSE 4.2 7.6 + - + -
47B GLU* 4.2 15.8 - - - +
48B GLY* 4.9 1.0 + - - -
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Residues in contact with GLU 88 (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 3.9 0.9 - - - +
8A ALA* 3.5 0.7 - - - -
9A GLN* 2.8 53.1 + - - +
51A ARG* 2.7 49.5 + - - +
87A ALA* 1.3 78.6 - - - +
89A MSE 1.3 65.5 + - - +
47B GLU 3.4 9.0 - - - +
48B GLY* 4.5 11.1 - - - -
49B THR 4.7 11.7 - - - +
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Residues in contact with MSE 89 (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* 3.3 41.5 - - + +
7A ILE 3.3 5.6 - - - +
8A ALA* 3.6 19.3 - - + -
10A VAL* 6.0 0.2 - - - -
21A TYR* 5.0 1.1 - - - +
69A TYR* 3.9 15.3 - - + -
74A TYR* 3.3 10.5 - - - +
81A ARG* 3.2 37.9 - - - +
87A ALA* 4.5 7.6 - - + -
88A GLU* 1.3 82.5 - - - +
90A MSE 1.3 63.7 + - - +
45B GLU* 4.0 0.7 - - - -
46B LEU* 3.0 31.4 + - + -
47B GLU* 2.8 25.6 + - + +
48B GLY 4.9 0.3 - - - +
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Residues in contact with MSE 90 (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* 3.4 5.2 - - - +
7A ILE* 2.8 60.9 + - + +
9A GLN* 4.1 9.6 - - - +
89A MSE 1.3 76.8 - - - +
91A ILE* 1.3 62.9 + - - +
92A VAL* 4.0 8.5 - - + -
7B ILE* 5.4 1.3 - - + -
9B GLN* 3.8 24.7 - - + +
43B VAL* 3.9 12.1 - - + -
44B THR 3.2 14.1 - - - +
45B GLU* 4.4 3.6 - - - -
46B LEU* 4.1 5.1 - - - +
50B ALA* 3.9 22.0 - - + -
54B ASN* 3.4 35.7 - - + +
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Residues in contact with ILE 91 (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* 4.2 0.4 - - - -
5A TYR 3.2 18.6 - - - +
6A TRP* 4.3 7.4 - - + -
62A VAL* 4.1 26.9 - - + -
65A ALA* 3.6 24.5 - - + +
66A ILE* 3.6 44.0 - - + +
90A MSE 1.3 77.9 - - - +
92A VAL* 1.3 62.5 + - - +
42B SER 3.6 1.2 - - - +
43B VAL* 3.3 4.0 - - - +
44B THR* 2.7 45.3 + - - -
46B LEU* 3.8 29.6 - - + -
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Residues in contact with VAL 92 (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 0.2 - - - -
5A TYR* 2.8 39.4 + - + +
7A ILE* 4.1 17.5 - - + -
90A MSE 4.0 17.9 - - + -
91A ILE* 1.3 79.1 - - - +
93A GLU* 1.3 67.8 + - - +
94A GLY 3.5 0.2 + - - -
38B ALA* 3.8 24.5 - - + -
41B GLY 4.0 17.9 - - - +
42B SER 3.5 2.2 - - - -
43B VAL* 4.4 3.1 - - + -
54B ASN* 3.7 38.1 - - + +
56B VAL* 5.4 0.7 - - + -
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Residues in contact with GLU 93 (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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1A MSE 5.0 7.4 - - - +
2A ALA* 3.6 27.5 - - + +
3A LYS 3.9 0.4 - - - +
62A VAL* 3.6 32.5 + - + +
92A VAL* 1.3 73.2 - - - +
94A GLY* 1.3 70.2 + - - +
38B ALA* 3.6 12.5 - - - +
39B ARG 4.9 0.2 + - - -
41B GLY* 3.8 15.0 - - - -
42B SER* 2.8 39.3 + - - +
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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