Contacts of the strand formed by residues 2 - 10 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1L ILE* 1.3 77.5 + - - +
3L LEU* 1.3 70.2 + - - +
4L LYS* 4.3 9.4 - - + +
24L HIS 4.4 0.4 - - - +
25L TYR* 3.2 12.0 - - - -
26L ASN* 2.7 53.6 + - - +
97L CYS 3.9 5.5 + - - +
98L TYR* 3.9 11.6 - - - +
107L TYR* 5.5 2.0 - - - +
167L ILE* 3.9 4.0 - - - -
210L PRO* 6.3 0.4 - - - -
211L ASP* 3.9 20.0 - - - +
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Residues in contact with LEU 3 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L THR* 1.3 75.7 - - - +
4L LYS* 1.3 60.3 + - - +
5L TYR* 4.0 15.0 - - + +
23L ASP* 3.6 24.5 - - - +
24L HIS 3.4 8.5 - - - +
25L TYR* 4.4 3.1 - - + -
96L GLY* 3.1 4.9 - - - -
97L CYS 2.9 32.3 + - - +
107L TYR* 3.4 2.1 + - - -
158L PHE* 4.6 0.2 - - + -
163L CYS* 3.9 22.2 - - - -
166L ALA* 4.3 5.2 - - + -
167L ILE* 3.8 42.1 - - + +
170L TYR* 3.7 35.7 - - + -
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Residues in contact with LYS 4 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2L THR* 4.2 9.2 - - + -
3L LEU* 1.3 74.3 - - - +
5L TYR* 1.3 77.9 + - - +
6L ASN* 4.2 6.3 - - + -
22L TYR 3.6 3.1 - - - +
24L HIS* 2.8 68.1 + - + +
94L ILE* 4.7 4.3 - - + -
95L THR 3.9 1.3 - - - +
107L TYR* 3.6 15.0 - - + +
248L PRO* 3.7 33.5 - - + +
325L NAG 3.1 26.6 + - - +
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Residues in contact with TYR 5 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L LEU* 4.0 13.5 - - + +
4L LYS* 1.3 84.1 - - - +
6L ASN* 1.3 60.5 + - - +
7L TYR* 4.2 9.6 - - + -
21L PHE* 3.9 17.9 - + + -
22L TYR 3.5 2.7 - - - -
23L ASP* 3.2 31.6 - - - -
59L THR* 3.4 14.6 + - - +
60L PRO* 3.7 18.1 - - + +
64L TYR* 3.7 8.7 - + - -
93L LEU 3.4 4.3 - - - +
94L ILE* 3.6 2.6 - - - -
95L THR* 2.7 49.2 + - + +
158L PHE* 3.1 40.4 - + - -
166L ALA* 5.2 0.3 - - - +
170L TYR* 2.7 24.3 + - - -
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Residues in contact with ASN 6 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L LYS* 5.1 8.7 - - - +
5L TYR* 1.3 74.3 - - - +
7L TYR* 1.3 65.1 + - - +
8L THR* 2.9 12.6 + - - -
20L VAL 3.7 1.2 - - - +
21L PHE* 3.1 7.4 - - - -
22L TYR* 2.9 53.1 + - + +
24L HIS* 5.9 0.7 - - + -
92L SER* 4.1 0.7 + - - -
93L LEU 3.7 2.0 - - - -
94L ILE* 3.3 17.7 - - + +
325L NAG 1.5 64.4 + - - +
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Residues in contact with TYR 7 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L TYR* 4.3 17.1 - + + -
6L ASN* 1.3 73.3 + - - +
8L THR* 1.3 63.4 + - - +
20L VAL 3.5 4.7 - - - +
21L PHE* 3.4 39.2 - + + -
60L PRO* 5.3 3.3 - - - +
64L TYR* 2.6 38.3 + - + +
66L PHE* 4.5 13.2 - + + -
69L TRP* 3.5 36.3 + + + -
70L TYR 5.6 0.2 - - - -
73L MET* 3.7 22.1 - - - +
92L SER* 3.1 5.7 - - - -
93L LEU* 2.8 59.9 + - + -
95L THR* 4.7 6.5 - - + -
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Residues in contact with THR 8 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L ASN* 2.9 17.7 + - - -
7L TYR* 1.3 73.0 + - - +
9L VAL* 1.3 68.9 + - - +
10L THR* 4.0 16.1 + - - +
18L ASP 3.6 0.7 - - - +
19L GLY* 3.2 2.3 - - - -
20L VAL* 2.8 55.7 + - + +
90L SER* 4.3 9.2 - - - +
91L LEU 3.3 6.1 - - - +
92L SER* 2.9 26.1 + - - +
325L NAG 3.6 19.8 + - - +
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Residues in contact with VAL 9 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L THR* 1.3 76.3 - - - +
10L THR* 1.3 60.3 + - - +
17L TYR* 5.1 4.5 - - + -
18L ASP 2.9 8.1 - - - +
19L GLY* 4.5 0.4 - - - -
70L TYR* 3.8 36.1 - - + +
73L MET* 3.8 42.1 - - + +
74L LYS* 4.3 4.3 - - - +
77L LEU* 3.6 21.0 - - + +
90L SER* 3.1 3.5 - - - -
91L LEU* 3.0 35.2 + - + +
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Residues in contact with THR 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L THR* 4.0 10.6 + - - +
9L VAL* 1.3 77.1 + - - +
11L LEU* 1.3 63.6 + - - +
12L LYS* 3.1 19.0 + - + +
17L TYR* 3.1 10.9 - - - -
18L ASP* 2.8 40.2 + - - +
20L VAL* 5.7 1.9 - - - +
77L LEU* 4.6 0.2 - - - -
89L THR* 3.5 24.5 - - + +
90L SER* 3.5 14.5 - - - -
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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