Contacts of the strand formed by residues 90 - 100 (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 SER 90 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8F THR* 4.3 10.9 - - - +
9F VAL 3.1 15.5 - - - -
10F THR* 3.5 19.4 - - - +
77F LEU* 4.1 7.3 - - - +
88F THR* 3.1 21.2 - - - +
89F THR* 1.3 83.8 - - - +
91F LEU* 1.3 62.6 + - - +
92F SER* 5.2 1.0 + - - -
112F THR* 3.8 3.7 + - - -
113F ALA* 3.5 22.1 + - - +
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Residues in contact with LEU 91 (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* 3.3 4.7 - - - +
9F VAL* 3.0 40.6 + - + -
73F MET* 3.4 19.6 - - + +
76F THR* 3.6 37.5 - - + -
77F LEU* 4.1 12.3 - - + +
80F ILE* 4.1 13.5 - - + -
90F SER* 1.3 75.9 - - - +
92F SER* 1.3 62.9 + - - +
110F VAL* 3.5 20.6 - - + -
111F GLU 3.5 16.8 - - - +
112F THR* 3.7 16.6 - - - +
117F LEU* 4.5 0.7 - - + -
140F MET* 4.0 12.3 - - + -
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Residues in contact with SER 92 (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* 4.0 6.6 + - - -
7F TYR 3.0 7.2 - - - -
8F THR* 2.8 29.0 + - - +
73F MET* 3.9 3.8 - - - -
90F SER* 5.2 1.7 + - - -
91F LEU* 1.3 74.1 - - - +
93F LEU* 1.3 61.1 + - - +
94F ILE* 3.8 6.0 + - - -
109F TYR 3.8 0.2 - - - +
110F VAL* 3.2 9.3 - - - +
111F GLU* 2.9 54.8 + - - +
325F NAG 4.5 6.8 + - - -
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Residues in contact with LEU 93 (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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5F TYR 3.4 6.6 - - - +
6F ASN* 3.6 0.5 - - - -
7F TYR* 2.7 56.0 + - + -
69F TRP* 3.7 48.5 - - + -
73F MET* 3.7 10.0 - - + +
92F SER* 1.3 71.6 - - - +
94F ILE* 1.3 63.2 + - - +
95F THR* 3.9 3.1 + - + -
109F TYR 3.6 14.1 - - - +
110F VAL* 3.8 17.9 - - + -
140F MET* 5.0 4.0 - - + -
155F LEU* 4.3 30.1 - - + -
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Residues in contact with ILE 94 (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* 4.7 4.9 - - + -
5F TYR 3.6 3.8 - - - +
6F ASN* 3.4 37.0 - - + +
92F SER* 4.2 5.4 - - - -
93F LEU* 1.3 73.4 - - - +
95F THR* 1.3 63.1 + - - +
107F TYR* 3.8 5.6 - - + -
108F GLY* 3.1 2.8 + - - -
109F TYR* 2.7 72.3 + - + +
111F GLU* 4.0 16.2 - - + -
248F PRO* 3.4 32.5 - - + -
325F NAG 3.7 18.8 - - + +
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Residues in contact with THR 95 (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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5F TYR* 2.7 59.0 + - + +
7F TYR* 4.7 10.8 - - + -
93F LEU* 5.0 5.2 - - + +
94F ILE* 1.3 76.9 - - - +
96F GLY* 1.3 52.5 + - - +
107F TYR* 2.8 26.3 + - - -
108F GLY* 4.0 0.2 - - - -
155F LEU* 3.7 28.1 - - + +
158F PHE* 3.8 23.2 - - + -
159F GLU* 4.7 4.2 - - - +
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Residues in contact with GLY 96 (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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3F LEU 3.1 13.7 - - - -
5F TYR 4.6 0.2 - - - -
95F THR* 1.3 76.7 + - - +
97F CYS* 1.3 60.8 + - - +
106F SER* 3.2 4.3 - - - -
107F TYR* 2.8 43.3 + - - +
158F PHE* 4.3 3.1 - - - -
159F GLU* 5.8 0.3 - - - -
163F CYS* 3.6 15.0 - - - -
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Residues in contact with CYS 97 (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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2F THR* 3.8 2.4 + - - +
3F LEU* 2.9 30.1 + - - +
96F GLY* 1.3 75.5 - - - +
98F TYR* 1.3 69.2 + - - +
105F GLY 3.1 15.7 - - - +
106F SER* 3.9 9.6 - - - +
107F TYR* 3.8 6.6 + - - -
163F CYS* 3.2 42.4 - - + -
164F SER* 3.8 10.5 - - - +
167F ILE* 3.8 24.0 - - - -
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Residues in contact with TYR 98 (chain F).
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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1F ILE 3.6 11.7 - - - +
2F THR* 3.9 9.4 - - - +
97F CYS* 1.3 85.6 - - - +
99F GLU* 1.3 62.5 + - - +
100F THR* 3.6 22.2 - - - +
103F LEU* 4.0 5.3 - - + +
104F PHE* 3.2 33.5 + - - +
105F GLY* 3.0 41.4 + - - +
106F SER 4.2 2.0 - - - -
107F TYR* 4.5 7.4 - + + -
167F ILE* 4.5 4.7 - - - -
211F ASP* 5.7 0.4 - - + -
213F ILE* 4.3 15.4 - - + +
245F PRO 3.9 11.1 + - - -
246F GLY* 3.6 34.3 - - - +
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Residues in contact with GLU 99 (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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31C ARG* 3.0 40.2 + - - +
32C ARG* 2.7 44.1 + - - -
1F ILE* 2.9 53.1 + - + +
98F TYR* 1.3 76.7 - - - +
100F THR* 1.3 59.2 + - - +
101F GLY 3.5 3.1 + - - +
103F LEU 3.5 5.4 - - - -
104F PHE* 4.1 8.5 - - + -
164F SER 5.4 0.7 - - - +
167F ILE* 5.0 7.7 - - + +
168F LEU* 4.0 7.3 - - - +
286F ASP* 3.0 7.8 - - - +
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Residues in contact with THR 100 (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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98F TYR* 3.6 21.6 - - - +
99F GLU* 1.3 68.8 - - - +
101F GLY* 1.3 65.8 + - - +
102F LEU 3.2 0.3 + - - -
103F LEU* 3.0 24.7 + - - +
211F ASP* 3.0 42.7 + - - +
212F VAL* 3.9 0.4 - - - +
213F ILE* 3.9 27.4 - - + +
284F PHE* 3.3 29.5 - - - +
285F HIS* 4.3 1.3 - - - -
286F 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