Contacts of the strand formed by residues 52 - 61 (chain B) in PDB entry 3SEA
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 GLN 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B GLN 4.2 12.5 + - - -
4B SER* 4.4 0.4 - - - +
5B LYS* 3.7 35.1 - - + +
48B THR* 3.3 3.0 - - - +
49B VAL 2.8 36.6 + - - +
50B ASN 2.9 5.7 + - - +
51B GLY* 1.3 81.5 - - - +
53B GLU* 1.3 79.8 + - - +
54B TYR* 3.3 36.7 - - + +
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Residues in contact with GLU 53 (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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3B GLN 4.2 11.3 + - - +
4B SER* 3.5 20.6 + - - +
5B LYS 3.3 12.5 + - - -
46B LEU* 3.9 32.2 - - + +
47B ILE 3.5 8.1 - - - +
48B THR* 4.0 15.3 + - + +
51B GLY 4.1 1.4 + - - -
52B GLN* 1.3 92.6 + - - +
54B TYR* 1.3 68.0 + - - +
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Residues in contact with TYR 54 (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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4B SER* 4.1 1.8 - - - -
5B LYS* 3.4 37.9 - - + +
7B ARG* 4.2 15.9 - - + -
45B LYS 3.6 2.1 - - - +
46B LEU* 3.3 7.4 - - - +
47B ILE* 2.7 40.5 + - + +
49B VAL* 3.9 14.0 + - + +
52B GLN* 3.3 42.6 - - + +
53B GLU* 1.3 73.4 - - - +
55B HIS* 1.3 60.8 + - - +
56B LEU* 3.6 17.4 + - + -
164B ILE* 3.7 36.6 - - + -
168B GLU* 3.2 28.2 + - - +
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Residues in contact with HIS 55 (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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4B SER* 3.6 17.7 + - - +
5B LYS 3.0 10.6 + - - +
6B SER* 3.3 23.4 + - - -
7B ARG 3.1 20.7 + - - -
44B THR* 3.8 35.5 - - - +
45B LYS 4.6 2.1 + - - -
46B LEU* 3.4 23.7 - - + +
54B TYR* 1.3 69.9 - - - +
56B LEU* 1.3 66.2 + - - +
57B GLN* 5.4 2.5 - - + -
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Residues in contact with LEU 56 (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 ARG* 3.5 26.5 - - + +
9B ILE* 4.6 6.5 - - + -
26B PHE* 4.1 21.3 - - + -
43B PHE 3.7 0.2 - - - +
44B THR* 3.0 11.0 - - - -
45B LYS* 2.8 40.8 + - + +
47B ILE* 3.8 21.1 - - + -
54B TYR* 3.9 10.8 - - + -
55B HIS* 1.3 76.5 - - - +
57B GLN* 1.3 60.4 + - - +
58B LEU* 3.8 23.3 - - + -
160B PHE* 4.4 9.9 - - + +
163B ILE* 5.7 0.4 - - + -
164B ILE* 3.9 27.6 - - + -
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Residues in contact with GLN 57 (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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6B SER* 5.3 6.8 + - - +
7B ARG 2.8 13.7 + - - +
8B LYS* 3.4 41.0 - - + +
9B ILE 2.8 28.4 + - - +
42B THR* 3.3 30.0 + - + +
43B PHE 3.5 2.9 - - - +
44B THR* 4.5 9.9 - - + +
55B HIS* 3.8 4.2 + - + +
56B LEU* 1.3 72.3 - - - +
58B LEU* 1.3 61.4 + - - +
59B VAL* 3.8 1.0 + - + -
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Residues in contact with LEU 58 (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 ILE* 3.6 13.9 - - + -
11B ILE* 3.9 11.4 - - + -
23B THR* 3.9 10.1 - - + -
26B PHE* 3.7 22.4 - - + -
27B VAL* 3.7 29.6 - - + -
41B ASN 3.6 0.3 - - - +
42B THR* 3.2 4.0 - - - -
43B PHE* 2.6 46.0 + - + +
45B LYS* 4.7 2.5 - - + -
56B LEU* 3.8 31.2 - - + +
57B GLN* 1.3 75.8 - - - +
59B VAL* 1.3 60.8 + - - +
60B ASP 3.4 3.7 + - - -
160B PHE* 3.8 26.7 - - + -
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Residues in contact with VAL 59 (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 LYS* 3.6 35.9 - - + +
9B ILE 2.7 19.0 + - - +
10B ALA* 3.6 5.6 - - + -
11B ILE* 2.9 28.3 + - - -
40B GLU* 4.2 17.5 - - + +
41B ASN 3.6 3.6 - - - +
42B THR* 4.0 14.1 - - + +
57B GLN 4.7 0.2 - - - +
58B LEU* 1.3 70.9 - - - +
60B ASP* 1.3 59.7 + - - +
61B THR* 3.6 19.8 + - + +
74B TYR* 3.9 20.2 - - + -
78B ILE* 4.8 3.6 - - + -
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Residues in contact with ASP 60 (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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1B ACT 4.7 1.6 - - - +
11B ILE* 4.3 6.8 - - + +
19B LYS* 3.5 15.2 - - - +
20B SER* 2.4 49.9 + - - -
23B THR* 4.4 8.5 + - - +
38B THR* 3.3 13.9 + - - +
40B GLU* 3.5 1.9 - - - +
41B ASN* 2.8 36.8 + - + +
43B PHE* 3.9 26.9 - - + -
58B LEU 3.4 1.8 + - - +
59B VAL* 1.3 70.2 - - - +
61B THR* 1.3 63.0 + - - +
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Residues in contact with THR 61 (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 ALA* 5.0 1.3 - - + -
11B ILE 2.7 27.8 + - - +
12B LEU* 3.5 20.3 - - + +
19B LYS* 3.4 16.3 - - - +
38B THR* 3.7 12.2 - - - -
39B ILE 4.6 1.8 - - - -
59B VAL* 3.7 17.9 - - + +
60B ASP* 1.3 79.1 + - - +
62B ALA* 1.3 70.4 + - - +
63B GLY 3.7 0.2 + - - -
64B GLN* 5.6 0.2 - - - -
74B TYR* 3.4 46.2 - - + +
179B GNP 4.1 0.2 + - - -
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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