Contacts of the strand formed by residues 6 - 14 (chain B) in PDB entry 3FHX
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 ARG 6 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ARG* 3.3 49.1 - - - +
287A MET* 5.9 2.4 + - - +
290A GLU* 6.2 2.2 - - - +
4B GLU* 3.8 35.0 + - + +
5B CYS* 1.3 72.2 - - - +
7B VAL* 1.3 61.8 + - - +
34B GLU* 3.4 30.9 + - + +
36B ASP* 3.7 12.1 + - - -
76B LYS 3.9 13.0 - - - +
77B TYR* 3.7 18.5 - - + +
78B ASP* 2.7 44.3 + - - +
79B TYR 3.0 8.5 + - - +
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Residues in contact with VAL 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 CYS 4.3 2.0 - - - +
6B ARG* 1.3 79.1 - - - +
8B LEU* 1.3 71.1 + - - +
28B LEU* 4.6 3.6 - - + -
33B PHE* 4.2 29.8 - - + -
34B GLU 3.0 6.3 + - - -
35B ILE* 3.4 24.6 - - + +
36B ASP* 2.8 30.7 + - - +
77B TYR* 3.6 4.2 - - - -
79B TYR* 3.4 25.4 - - + +
81B LEU* 4.3 7.2 - - + -
242B LEU* 4.0 24.7 - - + -
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Residues in contact with LEU 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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15A ILE* 4.1 7.4 - - + -
7B VAL* 1.3 71.2 - - - +
9B SER* 1.3 53.4 + - - +
10B ILE* 3.9 25.5 + - + -
36B ASP 3.7 11.2 - - - +
38B VAL* 3.8 22.0 - - + -
66B TYR* 5.4 4.0 - - + -
69B LEU* 4.7 6.5 - - + -
77B TYR* 3.4 39.3 - - + +
79B TYR 2.9 11.7 + - - +
80B VAL* 3.3 11.6 - - + +
81B LEU 2.7 32.8 + - - +
97B ILE* 4.6 7.9 - - + -
101B LEU* 3.9 22.7 - - + -
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Residues in contact with SER 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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7B VAL* 3.7 0.6 + - - -
8B LEU* 1.3 73.0 - - - +
10B ILE* 1.3 59.4 + - - +
11B GLN* 2.8 24.8 + - - -
21B ASN* 2.6 30.9 + - - +
24B ALA* 4.8 0.5 - - - +
35B ILE* 3.4 28.5 - - - +
36B ASP 2.9 12.3 + - - -
37B ALA* 3.5 0.4 - - - -
38B VAL* 2.8 23.8 + - - -
81B LEU* 3.2 12.7 - - - +
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Residues in contact with ILE 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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8B LEU* 3.9 22.6 + - + +
9B SER* 1.3 69.3 - - - +
11B GLN* 1.3 66.2 + - - +
38B VAL* 3.2 37.9 - - + +
40B SER* 4.5 2.6 - - - -
62B LEU* 4.3 13.7 - - + -
80B VAL* 5.1 4.9 - - + -
81B LEU 2.9 7.5 + - - -
82B THR* 3.7 25.2 - - + -
83B GLY 4.0 2.1 + - - -
84B TYR 5.6 0.2 - - - +
85B THR* 5.8 0.3 + - - -
90B PHE* 3.8 30.9 - - + -
94B VAL* 4.6 23.3 - - + -
97B ILE* 4.9 12.6 - - + -
98B VAL* 5.9 0.2 - - + -
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Residues in contact with GLN 11 (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 SER* 2.8 22.6 + - - +
10B ILE* 1.3 81.1 - - - +
12B SER* 1.3 59.8 + - - +
20B GLY* 3.8 15.3 - - - -
21B ASN* 3.1 31.5 + - - +
24B ALA* 3.8 13.7 - - - +
38B VAL 3.2 3.2 + - - -
39B ASN* 3.3 0.2 - - - -
40B SER* 2.7 33.5 + - - -
81B LEU* 3.4 28.1 - - - +
82B THR 4.5 2.2 - - - -
83B GLY* 3.8 26.4 - - - +
84B TYR 5.2 6.2 + - - +
235B ALA* 3.9 14.3 + - - +
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Residues in contact with SER 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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11B GLN* 1.3 77.6 - - - +
13B HIS* 1.3 60.6 + - - +
14B VAL* 5.4 0.2 - - - -
19B VAL* 3.8 4.3 - - - +
20B GLY* 3.4 7.7 - - - -
21B ASN* 2.6 31.8 + - - +
40B SER* 3.1 9.1 + - - -
41B VAL* 3.0 18.8 - - - +
84B TYR* 4.1 14.6 + - - +
313B PXL 3.0 42.5 + - - -
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Residues in contact with HIS 13 (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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37A ALA* 2.8 36.3 + - + +
39A ASN* 3.4 23.6 + - - -
11B GLN 4.0 0.2 + - - -
12B SER* 1.3 73.3 - - - +
14B VAL* 1.3 84.0 + - - +
19B VAL 5.3 0.2 - - - -
21B ASN* 4.8 1.6 - - + +
22B ARG* 3.2 31.1 + - + +
39B ASN* 3.4 31.8 + - + +
41B VAL* 3.0 25.0 + - - +
42B GLN* 3.3 18.1 - - + -
43B PHE 3.1 15.9 + - - -
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Residues in contact with VAL 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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13B HIS* 1.3 103.1 + - - +
15B ILE* 1.3 65.6 + - - +
16B ARG 3.1 22.0 - - - +
17B GLY 3.4 18.6 - - - +
19B VAL* 3.9 29.8 - - + -
22B ARG* 3.4 10.5 - - + +
43B PHE* 3.1 13.9 - - + +
45B ASN* 3.9 24.5 - - - +
46B HIS* 4.1 1.8 - - - +
313B PXL 4.5 8.7 - - + -
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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