Contacts of the strand formed by residues 89 - 94 (chain A) in PDB entry 5GQQ
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 89 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ILE* 4.1 17.2 - - + +
66A PHE* 3.6 24.9 - - + -
87A ALA* 4.3 0.4 - - - +
88A PRO* 1.3 70.8 - - - +
90A THR* 1.3 62.9 + - - +
107A ILE* 3.7 24.7 - - + -
108A SER 3.6 13.0 - - - +
109A LEU* 3.5 21.8 - - + -
176A THR* 4.4 1.2 + - - -
177A ALA* 3.2 1.4 - - - -
178A GLY* 2.6 42.1 + - - +
182A PRO* 5.6 3.1 - - + -
183A VAL* 4.4 6.7 - - + -
185A LEU* 3.7 15.7 - - + +
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Residues in contact with THR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TRP* 3.6 27.8 - - + -
62A ILE* 5.7 0.7 - - - -
88A PRO* 3.7 12.3 + - + -
89A VAL* 1.3 78.7 - - - +
91A SER* 1.3 63.0 + - - +
92A TYR* 5.9 0.2 - - - +
106A THR 5.1 0.2 + - - -
107A ILE* 3.4 7.8 - - - +
108A SER* 2.9 38.1 + - - +
132A ARG* 3.3 27.4 + - - +
175A TYR* 4.3 10.4 - - - -
176A THR* 3.0 14.4 - - - +
193A TRP* 4.0 13.5 - - + -
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Residues in contact with SER 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TRP* 2.9 26.2 + - - -
62A ILE* 4.7 4.0 - - - -
90A THR* 1.3 77.4 - - - +
92A TYR* 1.3 61.3 + - - +
93A VAL* 4.0 3.3 - - - +
105A ILE* 4.1 11.7 - - - -
106A THR 3.1 10.1 - - - -
107A ILE* 4.4 8.5 - - - -
174A TYR 3.7 0.3 - - - +
175A TYR* 3.0 11.3 - - - +
176A THR* 2.5 52.4 + - - +
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Residues in contact with TYR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A THR* 5.9 0.2 - - - +
91A SER* 1.3 75.7 - - - +
93A VAL* 1.3 62.2 + - - +
94A GLU* 3.8 35.6 + - + -
104A THR 3.4 5.4 - - - +
105A ILE* 3.5 1.0 - - - -
106A THR* 3.0 42.5 + - + +
132A ARG* 6.0 0.7 - - - +
173A VAL* 3.4 39.5 - - + +
174A TYR 3.4 9.4 - - - -
175A TYR* 3.5 45.1 - + + -
195A ILE* 4.0 5.5 - - + +
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TRP* 4.0 23.6 - - + -
91A SER* 4.0 9.2 - - - +
92A TYR* 1.3 77.7 - - - +
94A GLU* 1.3 61.4 + - - +
95A PRO* 5.9 0.2 - - + -
103A SER* 4.4 21.1 - - - +
104A THR 3.8 2.5 - - - -
105A ILE* 4.5 11.0 - - + +
172A LYS 4.1 1.9 - - - +
173A VAL* 3.3 27.2 - - - +
174A TYR* 3.0 52.7 + - + +
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A TYR* 3.8 28.5 + - + -
93A VAL* 1.3 74.5 - - - +
95A PRO* 1.3 69.5 - - + +
96A GLY 3.6 2.0 + - - +
103A SER* 3.3 5.8 - - - -
104A THR* 2.8 69.1 + - - +
106A THR* 4.4 5.5 + - - -
173A VAL* 3.7 13.5 - - + +
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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