Contacts of the strand formed by residues 89 - 94 (chain A) in PDB entry 2GB0
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
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Residue Dist Surf HB Arom Phob DC
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50A ILE* 4.0 19.1 - - + -
51A ILE 3.6 17.0 - - - +
52A ARG* 3.8 28.5 - - + -
88A GLY* 1.3 78.8 - - - +
90A LEU* 1.3 70.0 + - - +
91A VAL* 4.0 5.0 + - + +
139A ILE 4.0 0.7 - - - +
140A PHE* 3.5 5.0 - - - -
141A GLU* 2.9 36.4 + - + +
144A SER* 3.3 20.2 - - - +
145A GLY 3.7 9.6 - - - +
243A GLY 3.3 7.6 - - - +
244A PHE* 4.2 7.2 - - - -
245A MET 4.5 2.9 - - - +
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Residues in contact with LEU 90 (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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89A VAL* 1.3 72.4 - - - +
91A VAL* 1.3 68.0 + - - +
92A PHE* 3.8 22.7 - - + -
118A LEU* 5.1 0.4 - - + -
123A ILE* 4.5 2.5 - - + -
127A TRP* 3.6 36.1 - - + -
130A ILE* 3.6 31.4 - - + -
138A ALA* 3.9 21.3 - - + -
139A ILE 3.9 5.6 - - - +
140A PHE* 3.9 8.9 - - + -
242A PRO* 3.9 18.2 - - + -
243A GLY 2.9 9.9 + - - +
244A PHE* 3.2 10.7 - - + +
245A MET 3.0 24.6 + - - +
246A VAL* 4.0 0.9 - - - +
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Residues in contact with VAL 91 (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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52A ARG* 4.3 26.5 - - - +
89A VAL* 4.6 6.3 - - + +
90A LEU* 1.3 76.9 - - - +
92A PHE* 1.3 64.5 + - - +
100A PHE* 3.6 28.9 - - + -
101A VAL* 3.8 19.2 - - + +
104A THR* 4.1 12.3 - - + +
138A ALA* 3.1 5.2 - - - +
139A ILE* 2.8 53.0 + - + +
141A GLU* 6.0 2.9 - - + +
245A MET 3.3 13.0 - - - +
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Residues in contact with PHE 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 LEU* 3.8 23.8 - - + -
91A VAL* 1.3 76.8 - - - +
93A GLY* 1.3 62.0 + - - +
101A VAL* 3.5 11.3 - - - +
123A ILE* 4.5 9.0 - - + -
130A ILE* 4.0 15.5 - - + -
132A VAL* 3.5 31.2 - - + -
136A TYR* 3.8 20.4 - + + -
137A ASN 3.2 15.3 - - - +
138A ALA* 3.6 8.5 - - + -
246A VAL* 3.4 39.1 - - + +
247A GLU 3.0 25.2 + - - -
248A VAL* 4.6 3.8 - - + -
297A PHE* 4.6 8.3 - + - -
301A TYR* 4.5 13.0 - + + -
302A MET* 4.5 9.9 - - + -
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Residues in contact with GLY 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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92A PHE* 1.3 81.4 - - - +
94A PRO* 1.3 77.5 - - - +
98A SER* 4.6 1.6 - - - -
101A VAL* 3.7 10.8 - - - +
136A TYR* 3.3 12.1 - - - -
137A ASN* 3.0 28.5 + - - +
247A GLU 3.2 7.9 - - - -
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Residues in contact with PRO 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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93A GLY* 1.3 83.4 - - - +
95A LYS* 1.3 65.9 + - - +
96A GLY 3.3 0.5 + - - -
97A GLU* 3.0 44.2 + - + +
98A SER* 3.7 14.4 + - - -
135A ASN* 3.9 8.1 - - - +
136A TYR* 3.7 35.6 - - + +
137A ASN* 4.2 1.4 - - - +
247A GLU* 3.3 16.4 - - + +
248A VAL* 4.7 0.9 - - - -
249A PRO* 4.8 13.7 - - + -
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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