Contacts of the strand formed by residues 2 - 10 (chain E) in PDB entry 3IT8
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 THR 2 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E ILE* 1.3 78.0 + - - +
3E LEU* 1.3 69.7 + - - +
4E LYS* 4.3 10.3 - - + +
24E HIS 4.4 0.2 - - - +
25E TYR* 3.2 12.1 - - - -
26E ASN* 2.7 53.9 + - - +
97E CYS 3.9 4.1 + - - +
98E TYR* 3.9 11.4 - - - +
107E TYR* 5.5 1.6 - - - +
167E ILE* 3.9 4.5 - - - -
210E PRO* 6.3 0.9 - - + -
211E ASP* 3.9 20.2 - - - +
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Residues in contact with LEU 3 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E THR* 1.3 76.6 - - - +
4E LYS* 1.3 60.1 + - - +
5E TYR* 3.9 15.3 - - + +
23E ASP* 3.6 24.2 - - - +
24E HIS 3.4 9.4 - - - +
25E TYR* 4.4 2.7 - - + -
96E GLY* 3.1 4.7 - - - -
97E CYS* 2.9 33.1 + - - +
107E TYR* 3.5 2.1 + - - -
158E PHE* 4.6 0.4 - - + -
163E CYS* 3.9 21.5 - - - -
166E ALA* 4.2 5.8 - - + -
167E ILE* 3.8 42.8 - - + +
170E TYR* 3.7 35.0 - - + -
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Residues in contact with LYS 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E THR* 4.2 8.5 - - + -
3E LEU* 1.3 74.9 - - - +
5E TYR* 1.3 76.5 + - - +
6E ASN* 5.1 7.0 - - + +
22E TYR 3.6 3.1 - - - +
24E HIS* 2.8 68.4 + - + +
94E ILE* 4.7 4.7 - - + -
95E THR 3.9 1.1 - - - +
107E TYR* 3.6 16.6 - - + +
248E PRO* 3.7 33.1 - - + +
325E NAG 3.0 26.6 + - - +
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Residues in contact with TYR 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E LEU* 3.9 13.9 - - + +
4E LYS* 1.3 85.2 - - - +
6E ASN* 1.3 61.4 + - - +
7E TYR* 4.2 9.2 - + + -
21E PHE* 3.8 18.4 - + + -
22E TYR 3.5 2.7 - - - -
23E ASP* 3.2 30.7 - - - -
59E THR* 3.4 15.9 + - - +
60E PRO* 3.7 18.3 - - + +
64E TYR* 3.7 9.4 - + - -
93E LEU 3.4 4.2 - - - +
94E ILE* 3.6 2.4 - - - -
95E THR* 2.7 46.9 + - + +
158E PHE* 3.1 43.2 - + - -
166E ALA* 5.2 0.2 - - - +
170E TYR* 2.7 23.7 + - - -
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Residues in contact with ASN 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E LYS* 5.1 8.7 - - - +
5E TYR* 1.3 73.9 - - - +
7E TYR* 1.3 64.5 + - - +
8E THR* 2.8 16.3 + - - -
20E VAL 3.7 0.7 - - - +
21E PHE* 3.1 7.3 - - - -
22E TYR* 2.9 52.1 + - + +
24E HIS* 5.9 0.4 - - + -
92E SER* 4.1 0.5 - - - -
93E LEU 3.6 2.5 - - - -
94E ILE* 3.4 18.2 - - + +
325E NAG 1.4 64.6 + - - +
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Residues in contact with TYR 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E TYR* 4.3 16.3 - + + -
6E ASN* 1.3 74.4 + - - +
8E THR* 1.3 62.3 + - - +
20E VAL 3.5 4.5 - - - +
21E PHE* 3.4 40.0 - + + -
60E PRO* 5.3 3.3 - - - +
64E TYR* 2.6 37.2 + - + +
66E PHE* 4.5 14.4 - + + -
69E TRP* 3.5 37.9 + + + -
70E TYR 5.6 0.2 - - - -
73E MET* 3.7 20.8 - - - +
92E SER* 3.1 5.4 - - - -
93E LEU* 2.8 60.7 + - + -
95E THR* 4.7 6.3 - - + -
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Residues in contact with THR 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ASN* 2.8 22.2 + - - -
7E TYR* 1.3 70.9 - - - +
9E VAL* 1.3 67.9 + - - +
10E THR* 4.0 15.9 + - - +
18E ASP 3.7 0.5 - - - +
19E GLY* 3.2 3.1 - - - -
20E VAL* 2.8 53.8 + - + +
22E TYR* 6.0 0.2 - - - -
73E MET* 4.6 0.4 - - - -
90E SER* 4.3 9.4 - - - +
91E LEU 3.3 6.3 - - - +
92E SER* 3.0 20.8 + - - +
325E NAG 3.4 22.4 + - - -
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Residues in contact with VAL 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E THR* 1.3 75.1 - - - +
10E THR* 1.3 62.0 + - - +
17E TYR* 5.0 4.9 - - + -
18E ASP 2.9 8.7 - - - +
19E GLY* 4.5 0.4 - - - -
70E TYR* 3.8 35.2 - - + +
73E MET* 3.8 41.9 - - + +
74E LYS* 4.4 5.2 - - - +
77E LEU* 3.6 21.0 - - + +
90E SER* 3.1 4.0 - - - -
91E LEU* 3.0 36.2 + - + +
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Residues in contact with THR 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E THR* 4.0 10.2 + - - +
9E VAL* 1.3 76.8 + - - +
11E LEU* 1.3 63.0 + - - +
12E LYS* 3.1 20.1 + - + +
17E TYR* 3.0 11.5 - - - -
18E ASP* 2.8 40.1 + - - +
20E VAL* 5.7 2.3 - - - +
77E LEU* 4.6 0.2 - - - -
89E THR* 3.5 24.5 - - + +
90E SER* 3.6 14.5 - - - +
325E NAG 6.1 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
------------------------------------------------------------
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