Contacts of the strand formed by residues 91 - 96 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C TYR 3.8 0.5 - - - +
43C GLN* 3.6 1.9 - - - -
44C GLN* 2.7 46.4 + - + +
90C ALA* 1.4 75.0 - - - +
92C TYR* 1.3 62.9 + - - +
93C TYR* 3.6 35.9 + - + +
106C ALA 5.0 1.1 - - - +
107C GLY* 4.0 4.0 - - - -
108C THR 3.4 21.8 - - - +
109C LYS* 3.8 34.3 - - + +
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Residues in contact with TYR 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLN* 2.6 25.7 + - - -
21C MET* 3.7 24.2 - - - -
41C TRP* 4.6 4.7 - + + -
42C TYR 3.3 4.5 - - - +
43C GLN* 2.9 35.1 + - + -
53C LEU* 3.6 26.5 - - + -
68C PHE* 3.5 14.9 - + - -
79C LEU* 3.6 20.2 - - + -
81C ILE* 3.7 6.2 - - + +
88C ASP* 2.5 33.0 + - - +
90C ALA* 3.8 11.2 - - + -
91C VAL* 1.3 73.8 - - - +
93C TYR* 1.3 55.1 + - - +
107C GLY* 3.2 1.3 - - - -
108C THR 2.9 28.8 + - - +
110C LEU* 3.7 21.5 - - + -
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Residues in contact with TYR 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLN* 3.6 3.4 - - - -
41C TRP* 3.3 5.6 - - - -
42C TYR* 2.7 47.5 + - + +
44C GLN* 3.4 30.6 + - + -
91C VAL* 3.6 28.3 - - + +
92C TYR* 1.3 76.3 - - - +
94C CYS* 1.3 63.5 + - - +
104C PHE* 4.6 5.4 - - + -
105C GLY 3.3 21.3 - - - -
106C ALA 3.6 20.3 + - - -
107C GLY* 3.7 6.1 - - - -
41D GLN* 3.4 16.7 + - - -
45D GLN 3.6 12.3 + - - -
46D GLY* 3.8 13.7 - - - -
47D LEU* 3.8 30.1 - - + -
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Residues in contact with CYS 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C MET* 3.9 13.9 - - - +
6C GLN* 3.3 22.6 + - - -
23C CYS* 2.1 52.9 - - + -
39C LEU* 4.5 2.2 - - + -
40C ALA 3.2 11.0 - - - +
41C TRP* 3.9 16.6 - - + -
93C TYR* 1.3 75.1 - - - +
95C GLN* 1.3 60.6 + - - +
104C PHE* 3.4 5.5 - - - +
105C GLY 2.9 25.1 + - - -
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Residues in contact with GLN 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C MET* 4.5 6.3 - - - -
39C LEU* 3.4 5.0 - - - +
40C ALA* 2.9 39.3 + - - +
42C TYR* 2.6 39.9 + - + -
94C CYS* 1.3 75.8 - - - +
96C GLN* 1.3 75.9 - - - +
97C TYR* 3.8 17.9 + - - +
102C LEU* 3.9 7.6 - - - +
103C THR 3.3 16.2 - - - +
104C PHE* 3.6 25.1 - - + -
111D MET* 3.4 29.2 - - - +
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Residues in contact with GLN 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ILE* 3.7 24.7 - - + +
4C MET* 3.8 13.5 - - - +
29C LEU* 3.6 28.5 - - + -
38C TYR 3.3 5.2 - - - -
95C GLN* 1.3 85.3 - - - +
97C TYR* 1.3 59.9 + - - +
98C TYR* 2.9 28.4 + - - +
99C SER 3.0 18.6 + - - -
101C PRO 2.9 27.9 + - - -
102C LEU* 3.9 2.6 - - - -
103C THR* 3.0 40.2 + - - +
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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