Contacts of the strand formed by residues 2 - 10 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1F ILE* 1.3 77.9 + - - +
3F LEU* 1.3 69.7 + - - +
4F LYS* 4.3 10.5 - - + +
24F HIS 4.4 0.4 - - - +
25F TYR* 3.2 11.1 - - - -
26F ASN* 2.7 55.4 + - - +
97F CYS 3.8 4.7 + - - +
98F TYR* 3.9 13.0 - - - +
107F TYR* 5.5 1.8 - - - +
167F ILE* 3.9 3.8 - - - -
210F PRO* 6.3 0.7 - - - -
211F ASP* 3.9 18.4 - - - +
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Residues in contact with LEU 3 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F THR* 1.3 74.5 - - - +
4F LYS* 1.3 61.1 + - - +
5F TYR* 4.0 14.8 - - + +
23F ASP* 3.6 24.0 - - - +
24F HIS 3.4 9.4 - - - +
25F TYR* 4.4 3.1 - - + -
96F GLY* 3.1 4.2 - - - -
97F CYS 2.9 35.1 + - - +
107F TYR* 3.5 2.1 + - - -
158F PHE* 4.6 0.4 - - + -
163F CYS* 3.9 20.9 - - - -
166F ALA* 4.2 5.6 - - + -
167F ILE* 3.8 36.7 - - + +
170F TYR* 3.7 41.3 - - + -
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Residues in contact with LYS 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F THR* 4.2 9.2 - - + -
3F LEU* 1.3 75.1 - - - +
5F TYR* 1.3 77.2 + - - +
6F ASN* 5.1 6.7 - - + +
22F TYR 3.5 2.9 - - - +
24F HIS* 2.8 67.5 + - + +
94F ILE* 4.7 3.6 - - + -
95F THR 3.9 1.1 - - - +
107F TYR* 3.6 13.9 - - + +
248F PRO* 3.7 32.7 - - + +
325F NAG 3.1 25.2 + - - +
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Residues in contact with TYR 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F LEU* 4.0 12.9 - - + +
4F LYS* 1.3 85.0 - - - +
6F ASN* 1.3 59.6 + - - +
7F TYR* 4.3 9.9 - - + -
21F PHE* 3.9 17.9 - + + -
22F TYR 3.5 2.7 - - - -
23F ASP* 3.2 31.0 - - - -
59F THR* 3.4 15.2 + - - +
60F PRO* 3.7 17.4 - - + +
64F TYR* 3.7 9.9 - + - -
93F LEU 3.4 4.5 - - - +
94F ILE* 3.6 2.8 - - - -
95F THR* 2.7 48.4 + - + +
158F PHE* 3.1 41.5 - + - -
166F ALA* 5.2 0.2 - - - +
170F TYR* 2.7 24.2 + - - -
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Residues in contact with ASN 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F LYS* 5.1 8.9 - - - +
5F TYR* 1.3 74.3 - - - +
7F TYR* 1.3 64.3 + - - +
8F THR* 2.9 16.5 + - - -
20F VAL 3.7 0.9 - - - +
21F PHE* 3.1 7.1 - - - -
22F TYR* 2.9 53.3 + - + +
24F HIS* 5.9 0.4 - - + -
92F SER* 4.0 0.3 + - - -
93F LEU 3.6 2.2 - - - -
94F ILE* 3.4 18.0 - - + +
325F NAG 1.5 64.8 + - - +
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Residues in contact with TYR 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F TYR* 4.3 17.0 - + + -
6F ASN* 1.3 74.4 + - - +
8F THR* 1.3 61.8 + - - +
20F VAL 3.5 4.9 - - - +
21F PHE* 3.4 39.4 - + + -
60F PRO* 5.2 3.5 - - - +
64F TYR* 2.6 38.0 + - + +
66F PHE* 4.5 14.6 - + + -
69F TRP* 3.5 36.1 + + + -
73F MET* 3.7 19.9 - - - +
92F SER* 3.0 5.7 - - - -
93F LEU* 2.7 60.7 + - + -
95F THR* 4.7 7.0 - - + -
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Residues in contact with THR 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ASN* 2.9 17.9 + - - -
7F TYR* 1.3 72.0 - - - +
9F VAL* 1.3 67.5 + - - +
10F THR* 4.1 16.1 + - - +
18F ASP 3.6 0.3 - - - +
19F GLY* 3.2 2.6 - - - -
20F VAL* 2.8 55.5 + - + +
73F MET* 4.6 0.4 - - - -
90F SER* 4.3 9.4 - - - +
91F LEU 3.3 7.2 - - - +
92F SER* 2.8 25.8 + - - +
325F NAG 3.6 19.7 - - - -
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Residues in contact with VAL 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F THR* 1.3 75.2 - - - +
10F THR* 1.3 61.6 + - - +
17F TYR* 5.0 5.4 - - + -
18F ASP 2.9 8.5 - - - +
19F GLY* 4.5 0.7 - - - -
70F TYR* 3.8 36.6 - - + +
73F MET* 3.8 41.1 - - + +
74F LYS* 4.4 4.5 - - - +
77F LEU* 3.6 21.5 - - + +
90F SER* 3.1 3.7 - - - -
91F LEU* 3.0 36.0 + - + +
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Residues in contact with THR 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F THR* 4.1 10.0 + - - +
9F VAL* 1.3 76.1 + - - +
11F LEU* 1.3 64.2 + - - +
12F LYS* 3.1 20.3 + - + +
17F TYR* 3.0 10.8 - - - -
18F ASP* 2.8 39.2 + - - +
20F VAL* 5.7 2.1 - - - +
77F LEU* 4.6 0.2 - - - -
89F THR* 3.5 24.5 - - + +
90F SER* 3.5 14.8 - - - -
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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