Contacts of the strand formed by residues 91 - 96 (chain F) in PDB entry 3Q3G
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 VAL 91 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42F TYR 3.8 0.5 - - - +
43F GLN* 3.5 1.7 - - - -
44F GLN* 2.7 46.5 + - + +
90F ALA* 1.3 75.0 - - - +
92F TYR* 1.3 64.2 + - - +
93F TYR* 3.6 36.5 + - + +
106F ALA 5.1 0.9 - - - +
107F GLY* 4.1 4.5 - - - -
108F THR 3.4 21.8 - - - +
109F LYS* 3.7 33.7 - - + +
44H GLU* 5.1 8.7 - - - +
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Residues in contact with TYR 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 GLN* 3.0 18.3 + - - -
21F MET* 3.8 25.8 - - - -
41F TRP* 4.6 9.6 - + + -
42F TYR 3.3 5.4 - - - +
43F GLN* 2.9 34.1 + - + -
53F LEU* 3.6 32.3 - - + -
68F PHE* 3.7 6.3 - + - -
79F LEU* 3.9 9.2 - - + -
81F ILE* 3.7 12.2 - - + +
88F ASP* 2.5 38.6 + - - +
90F ALA 3.8 11.4 - - - -
91F VAL* 1.3 75.1 - - - +
93F TYR* 1.3 62.7 + - - +
107F GLY* 3.2 0.9 - - - -
108F THR* 2.9 31.7 + - - +
110F LEU* 3.7 17.0 - - + -
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Residues in contact with TYR 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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6F GLN* 3.3 5.8 - - - -
41F TRP* 3.3 6.8 - - - -
42F TYR* 2.7 46.5 + - + +
44F GLN* 3.4 28.9 + - + -
50F PRO* 5.4 0.2 - - + -
91F VAL* 3.6 28.5 - - + +
92F TYR* 1.3 75.7 - - - +
94F CYS* 1.3 62.9 + - - +
104F PHE* 4.6 5.8 - - + -
105F GLY 3.4 18.2 - - - -
106F ALA 3.6 20.5 + - - -
107F GLY* 3.7 7.6 - - - -
41H GLN* 3.3 16.8 + - - -
44H GLU* 3.5 15.6 + - - -
46H GLY* 3.6 20.2 - - - -
47H LEU* 3.7 32.3 - - + -
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Residues in contact with CYS 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 MET* 4.1 12.1 - - - -
6F GLN* 3.0 23.9 + - - -
23F CYS* 2.0 52.9 - - + -
39F LEU* 4.5 2.5 - - + -
40F ALA 3.2 9.9 - - - +
41F TRP* 3.9 17.0 - - + -
93F TYR* 1.3 74.5 - - - +
95F GLN* 1.3 61.3 + - - +
104F PHE* 3.4 5.6 - - - +
105F GLY 2.9 25.1 + - - -
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Residues in contact with GLN 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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4F MET* 4.2 6.3 - - - -
39F LEU* 3.4 5.0 - - - +
40F ALA* 2.8 39.7 + - - +
42F TYR* 2.6 39.2 + - + -
94F CYS* 1.3 76.2 - - - +
96F GLN* 1.3 76.2 + - - +
97F TYR* 3.8 18.4 + - - +
102F LEU* 3.9 8.1 - - - +
103F THR 3.3 15.7 - - - +
104F PHE* 3.6 25.8 - - + -
111H MET* 3.4 27.9 - - - +
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Residues in contact with GLN 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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2F ILE* 3.7 23.0 - - + +
4F MET* 3.8 21.1 - - + +
29F LEU* 3.8 21.5 - - + -
38F TYR 3.3 4.9 - - - -
95F GLN* 1.3 84.9 - - - +
97F TYR* 1.3 60.2 + - - +
98F TYR* 2.9 28.4 + - - +
99F SER* 3.0 18.7 + - - -
101F PRO 2.9 28.1 + - - -
102F LEU* 3.9 2.8 - - - -
103F THR* 3.0 40.6 + - - +
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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