Contacts of the strand formed by residues 90 - 100 (chain J) 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 SER 90 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8J THR* 4.3 9.7 - - - +
9J VAL 3.1 15.5 - - - -
10J THR* 3.5 20.0 - - - +
77J LEU* 4.1 7.5 - - - +
88J THR* 3.1 21.9 - - - +
89J THR* 1.3 81.4 - - - +
91J LEU* 1.3 64.3 + - - +
92J SER* 5.1 1.4 + - - -
112J THR* 3.8 3.3 + - - -
113J ALA* 3.5 21.4 + - - +
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Residues in contact with LEU 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J THR* 3.3 4.5 - - - +
9J VAL* 3.0 40.6 + - + -
73J MET* 3.4 20.6 - - + +
76J THR* 3.6 36.1 - - + -
77J LEU* 4.0 12.1 - - + +
80J ILE* 4.1 13.7 - - + -
90J SER* 1.3 77.3 - - - +
92J SER* 1.3 63.0 + - - +
110J VAL* 3.5 20.9 - - + -
111J GLU 3.4 17.0 - - - +
112J THR* 3.7 15.9 - - - +
117J LEU* 4.5 1.1 - - + -
140J MET* 4.0 12.6 - - + -
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Residues in contact with SER 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J ASN* 4.0 7.0 + - - -
7J TYR 3.1 7.4 - - - -
8J THR* 2.9 27.8 + - - +
73J MET* 3.9 4.0 - - - -
90J SER* 5.1 1.6 + - - -
91J LEU* 1.3 73.9 - - - +
93J LEU* 1.3 59.9 + - - +
94J ILE* 3.9 6.7 + - - -
109J TYR 3.9 0.2 - - - +
110J VAL* 3.3 8.6 - - - +
111J GLU* 2.9 55.1 + - - +
325J NAG 4.4 6.5 - - - -
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Residues in contact with LEU 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J TYR 3.4 5.9 - - - +
6J ASN* 3.6 0.7 - - - -
7J TYR* 2.8 56.2 + - + -
69J TRP* 3.7 48.7 - - + -
73J MET* 3.7 10.5 - - + +
92J SER* 1.3 72.5 - - - +
94J ILE* 1.3 62.4 + - - +
95J THR* 3.9 3.8 + - + -
109J TYR 3.7 14.1 - - - +
110J VAL* 3.9 17.7 - - + -
140J MET* 5.0 4.0 - - + -
155J LEU* 4.3 29.4 - - + -
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Residues in contact with ILE 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J LYS* 4.7 3.6 - - + -
5J TYR 3.6 3.6 - - - +
6J ASN* 3.4 30.3 - - + +
92J SER* 4.2 6.5 - - - -
93J LEU* 1.3 73.5 - - - +
95J THR* 1.3 63.9 + - - +
107J TYR* 3.8 5.1 - - + -
108J GLY* 3.2 1.9 - - - -
109J TYR* 2.8 70.9 + - + +
111J GLU* 4.0 13.0 - - + -
248J PRO* 3.5 33.4 - - + -
325J NAG 3.2 29.6 - - + +
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Residues in contact with THR 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J LYS 3.7 0.3 - - - -
5J TYR* 2.7 54.7 + - + +
7J TYR* 4.7 10.8 - - + -
93J LEU* 5.0 5.4 - - + +
94J ILE* 1.3 77.0 - - - +
96J GLY* 1.3 53.2 + - - +
107J TYR* 2.8 26.2 + - - -
108J GLY* 3.9 4.7 - - - -
155J LEU* 3.7 21.9 - - + +
158J PHE* 3.7 23.4 - - + -
159J GLU* 4.7 4.2 - - - +
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Residues in contact with GLY 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J LEU* 3.1 13.5 - - - -
5J TYR 4.6 0.2 - - - -
95J THR* 1.3 77.4 + - - +
97J CYS* 1.3 61.1 + - - -
106J SER* 3.3 3.8 - - - -
107J TYR* 2.8 43.9 + - - +
158J PHE* 4.3 2.9 - - - -
159J GLU* 5.8 0.2 - - - -
163J CYS* 3.5 15.0 - - - -
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Residues in contact with CYS 97 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2J THR* 3.8 2.3 + - - +
3J LEU* 2.9 29.5 + - - +
96J GLY* 1.3 75.5 - - - +
98J TYR* 1.3 68.9 + - - +
105J GLY 3.2 15.9 - - - +
106J SER* 3.9 9.4 - - - +
107J TYR* 4.1 5.3 + - - -
163J CYS* 3.1 42.4 - - + -
164J SER* 3.9 10.8 - - - +
167J ILE* 3.8 23.8 - - - -
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Residues in contact with TYR 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1J ILE 3.5 11.7 - - - +
2J THR* 3.9 9.9 - - - +
97J CYS* 1.3 82.8 - - - +
99J GLU* 1.3 62.6 + - - +
100J THR* 3.6 22.4 - - - +
103J LEU* 4.0 9.8 - - + +
104J PHE* 3.2 33.4 + - - +
105J GLY* 3.0 42.5 + - - +
106J SER 4.1 2.0 - - - -
107J TYR* 4.5 6.7 - + + -
167J ILE* 4.5 4.7 - - - -
211J ASP* 5.7 0.7 - - + -
213J ILE* 4.3 11.5 - - + +
245J PRO 4.0 9.6 + - - -
246J GLY* 3.6 36.1 - - - +
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Residues in contact with GLU 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G ARG* 3.2 40.5 + - - +
32G ARG* 2.7 42.9 + - - -
1J ILE* 2.9 53.6 + - + +
98J TYR* 1.3 75.0 - - - +
100J THR* 1.3 60.5 + - - +
101J GLY 3.5 2.8 + - - +
103J LEU 3.5 4.7 - - - -
104J PHE* 4.1 7.9 - - + -
164J SER 5.4 1.0 - - - +
167J ILE* 5.0 7.7 - - + +
168J LEU* 4.0 7.1 - - - +
286J ASP* 3.0 8.0 - - - +
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Residues in contact with THR 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98J TYR* 3.6 22.2 - - - +
99J GLU* 1.3 68.1 - - - +
101J GLY* 1.3 65.9 + - - +
102J LEU 3.2 0.2 + - - -
103J LEU* 3.0 25.1 + - - +
211J ASP* 3.1 43.3 + - - +
212J VAL 4.1 0.9 - - - +
213J ILE* 3.9 26.5 - - + +
284J PHE* 3.2 30.0 - - - +
285J HIS* 4.3 1.6 - - - -
286J ASP* 4.0 0.7 - - - -
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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