Contacts of the strand formed by residues 63 - 71 (chain B) in PDB entry 1T0P
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 SER 63 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B THR* 4.5 2.3 + - - -
39B SER* 3.5 21.5 + - - -
40B LEU* 3.8 33.0 - - - +
61B GLY 3.4 7.0 + - - -
62B ASN* 1.3 76.3 - - - +
64B ARG* 1.3 66.3 + - - +
65B ILE* 4.9 0.4 - - - -
81B ASN* 5.0 0.2 - - - -
82B ILE* 2.9 41.9 + - - +
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Residues in contact with ARG 64 (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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140A MET* 3.5 49.5 - - + +
204A LEU* 6.4 0.9 - - - +
37B GLU 4.3 0.5 - - - +
38B THR* 4.7 2.4 + - - -
39B SER* 5.3 0.5 + - - -
63B SER* 1.3 78.1 + - - +
65B ILE* 1.3 69.8 + - - +
66B LEU* 4.0 15.0 - - + +
79B SER* 3.6 13.7 + - - -
80B SER 3.8 4.5 - - - +
81B ASN* 3.1 23.2 + - + +
302B NAG 3.1 69.9 + - + +
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Residues in contact with ILE 65 (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* 4.2 3.6 - - + -
9B PRO 5.9 0.2 - - - +
22B VAL* 3.7 40.6 - - + -
36B LEU* 4.0 14.4 - - + -
37B GLU 3.4 6.7 - - - +
38B THR* 3.4 26.9 - - - +
40B LEU* 4.7 1.8 - - + -
56B LEU* 4.2 6.7 - - + -
63B SER 4.6 1.1 - - - +
64B ARG* 1.3 78.4 - - - +
66B LEU* 1.3 67.5 + - - +
79B SER* 3.5 4.0 - - - -
80B SER* 3.0 56.9 + - - +
82B ILE* 4.0 24.0 - - + -
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Residues in contact with LEU 66 (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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140A MET* 4.4 12.8 - - + -
203A LEU 3.8 9.0 - - - +
204A LEU* 3.8 47.8 - - + +
205A LEU* 4.1 12.1 - - + -
7B VAL* 5.6 0.2 - - - -
36B LEU* 3.3 6.3 - - - +
37B GLU* 2.6 47.6 + - + +
64B ARG* 4.0 16.2 - - - +
65B ILE* 1.3 77.6 - - - +
67B CYS* 1.3 59.3 + - - +
77B THR* 4.2 10.5 - - + +
78B GLY 3.3 5.6 - - - +
79B SER* 3.5 27.8 - - - -
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Residues in contact with CYS 67 (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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205A LEU* 4.8 0.9 - - - -
5B LEU* 3.4 10.3 - - + -
7B VAL* 4.0 11.0 - - + +
24B CYS* 2.0 53.2 - - + -
34B ILE* 4.9 1.1 - - - -
35B ALA 3.2 13.2 - - - -
36B LEU* 3.3 26.2 - - - -
54B PHE* 4.8 1.3 - - - -
66B LEU* 1.3 74.5 - - - +
68B SER* 1.3 59.3 + - - +
77B THR* 2.7 22.6 + - - -
78B GLY 2.8 16.7 + - - -
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Residues in contact with SER 68 (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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205A LEU* 3.6 27.5 - - - +
243A THR* 3.9 18.4 + - - +
5B LEU* 3.5 4.6 - - - +
33B LYS 4.2 1.6 + - - -
34B ILE* 3.3 3.5 - - - +
35B ALA* 2.9 45.6 + - - +
67B CYS* 1.3 76.5 - - - +
69B VAL* 1.3 65.0 + - - +
70B TYR* 6.2 0.2 - - - -
75B GLN* 4.1 9.4 + - - -
76B ILE 3.2 10.1 - - - -
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Residues in contact with VAL 69 (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 LEU* 3.8 17.9 - - + -
26B THR* 4.2 7.9 - - + -
31B SER* 3.9 19.7 - - - -
32B GLU 3.1 20.9 - - - +
33B LYS 3.5 7.6 - - - +
34B ILE* 3.4 28.3 - - + -
68B SER* 1.3 78.7 - - - +
70B TYR* 1.3 65.4 + - - +
71B CYS* 5.2 0.2 - - + -
75B GLN* 3.4 2.4 - - - +
76B ILE* 2.9 55.0 + - + +
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Residues in contact with TYR 70 (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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207A ASN* 4.1 1.9 + - - -
243A THR 3.6 20.6 - - - -
244A ASP* 3.2 30.3 - - + +
245A SER* 5.1 7.2 - - - -
30B SER 4.7 0.7 - - - +
31B SER* 3.6 6.2 - - - -
32B GLU* 2.8 53.3 + - + +
33B LYS* 4.8 8.7 - - + -
69B VAL* 1.3 76.6 - - - +
71B CYS* 1.3 59.9 + - - +
72B ASN 4.0 1.5 + - - -
73B GLY* 3.6 30.3 - - - +
74B SER 3.3 2.7 - - - -
75B GLN* 3.4 39.9 + - + +
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Residues in contact with CYS 71 (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 GLN 4.1 13.2 - - - +
3B PHE* 3.3 24.0 - - - -
28B CYS* 2.0 51.4 - - + -
31B SER* 5.2 0.4 - - - +
69B VAL* 3.8 1.3 + - + -
70B TYR* 1.3 71.8 - - - +
72B ASN* 1.3 75.5 + - - +
73B GLY 3.2 0.2 - - - -
74B SER* 2.6 27.2 + - - +
76B ILE* 4.0 25.0 - - + +
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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