Contacts of the strand formed by residues 74 - 84 (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 74 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B TYR* 3.3 4.0 - - - -
71B CYS* 2.6 41.4 + - - +
72B ASN* 4.0 5.9 + - - +
73B GLY* 1.3 79.7 - - - +
75B GLN* 1.3 64.3 + - - +
76B ILE* 3.6 5.4 + - - +
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Residues in contact with GLN 75 (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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175A THR* 4.1 6.9 - - - +
205A LEU* 3.4 23.5 - - + +
207A ASN* 3.0 41.1 + - - -
243A THR* 3.4 15.2 + - - -
68B SER* 4.1 10.5 - - - -
69B VAL 3.4 10.1 - - - +
70B TYR* 3.4 33.4 + - + +
74B SER* 1.3 74.3 - - - +
76B ILE* 1.3 71.0 + - - +
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Residues in contact with ILE 76 (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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2B GLU* 6.0 1.8 - - - +
3B PHE* 3.7 27.6 - - + +
4B LEU 4.1 3.1 - - - -
5B LEU* 3.7 19.9 - - + +
26B THR* 4.2 7.9 - - - +
68B SER* 3.2 6.4 - - - -
69B VAL* 2.9 59.1 + - + +
71B CYS* 4.0 22.4 - - + +
74B SER* 4.3 9.6 - - - +
75B GLN* 1.3 79.5 - - - +
77B THR* 1.3 63.5 + - - +
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Residues in contact with THR 77 (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* 4.4 18.6 - - + +
5B LEU* 4.0 12.7 + - - +
66B LEU* 4.2 14.3 - - + +
67B CYS 2.7 21.0 + - - -
76B ILE* 1.3 79.0 - - - +
78B GLY* 1.3 63.8 + - - +
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Residues in contact with GLY 78 (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* 3.5 23.7 - - - +
7B VAL* 3.5 12.5 - - - +
66B LEU* 3.3 3.3 - - - -
67B CYS 2.8 31.5 + - - +
77B THR* 1.3 79.2 + - - +
79B SER* 1.3 59.9 + - - -
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Residues in contact with SER 79 (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 6.2 - - - +
10B GLN* 2.8 28.7 + - - +
64B ARG* 3.6 13.7 + - - -
65B ILE 3.5 5.2 - - - -
66B LEU* 3.5 23.1 - - - -
78B GLY* 1.3 74.2 - - - -
80B SER* 1.3 63.8 + - - +
302B NAG 2.9 35.2 + - - -
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Residues in contact with SER 80 (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* 3.5 22.9 - - - -
9B PRO 2.9 21.9 + - - -
10B GLN* 3.9 2.7 - - - -
11B ASN* 3.0 18.5 + - - +
12B PRO* 3.3 7.3 - - - +
64B ARG* 3.8 0.2 - - - -
65B ILE* 3.0 43.7 + - - +
79B SER* 1.3 79.6 - - - +
81B ASN* 1.3 64.4 + - - +
82B ILE* 3.6 2.9 + - - +
302B NAG 4.3 0.2 - - - -
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Residues in contact with ASN 81 (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 ASN* 2.8 38.2 - - + +
12B PRO 3.6 1.4 - - - +
63B SER 4.2 2.9 - - - -
64B ARG* 3.1 31.6 + - + +
80B SER* 1.3 70.8 + - - +
82B ILE* 1.3 64.7 + - - +
83B THR* 3.6 7.8 + - - +
302B NAG 1.5 69.5 + - - +
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Residues in contact with ILE 82 (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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12B PRO* 3.7 12.1 - - + +
14B LEU* 3.6 26.9 - - + -
20B LEU* 3.6 26.0 - - + -
40B LEU* 4.1 12.1 - - + -
56B LEU* 4.1 12.1 - - + -
59B VAL* 4.2 17.3 - - + -
62B ASN* 3.3 6.8 - - - +
63B SER 2.9 42.7 + - - +
65B ILE* 4.0 25.6 - - + -
80B SER* 4.5 6.7 - - - +
81B ASN* 1.3 72.3 - - - +
83B THR* 1.3 62.5 + - - +
84B VAL* 4.3 3.8 - - + -
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Residues in contact with THR 83 (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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12B PRO 3.0 13.5 + - - -
13B VAL* 3.3 24.8 - - + +
14B LEU* 2.9 30.1 + - - +
62B ASN* 3.6 17.3 + - - +
81B ASN* 4.1 9.0 + - - +
82B ILE* 1.3 75.2 + - - +
84B VAL* 1.3 70.0 + - - +
85B TYR* 5.7 1.8 - - + -
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Residues in contact with VAL 84 (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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14B LEU* 3.2 17.5 - - + +
15B SER 4.2 5.4 - - - +
16B ALA 4.0 21.3 - - - +
59B VAL* 3.9 23.6 - - + +
60B THR 4.4 11.0 - - - +
61B GLY* 3.5 28.9 - - - +
62B ASN* 2.7 23.2 + - - +
82B ILE* 4.3 2.0 - - + -
83B THR* 1.3 82.2 - - - +
85B TYR* 1.3 69.4 + - - +
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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