Contacts of the helix formed by residues 91 - 103 (chain A) in PDB entry 2GPC
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 THR 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A GLU 4.6 5.4 - - - +
90A PRO* 1.3 78.3 - - - +
92A GLY* 1.3 68.1 + - - +
93A LYS 3.6 1.2 + - - -
94A VAL* 3.7 7.8 + - - +
95A ALA* 3.4 14.5 + - - -
191A GLU* 5.4 3.3 - - - +
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Residues in contact with GLY 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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91A THR* 1.3 76.8 - - - +
93A LYS* 1.3 59.4 + - - -
95A ALA* 3.3 4.6 + - - +
96A ASP* 3.0 36.1 + - - +
191A GLU* 6.4 0.4 - - - -
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Residues in contact with LYS 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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91A THR 3.6 0.6 + - - -
92A GLY* 1.3 68.5 - - - -
94A VAL* 1.3 61.0 + - - +
96A ASP* 3.2 15.6 + - + +
97A GLU* 2.9 71.8 + - + +
191A GLU* 4.9 15.3 + - + +
194A LEU* 3.9 13.7 - - + -
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Residues in contact with VAL 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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90A PRO* 3.5 29.6 - - + -
91A THR 3.7 4.9 + - - +
92A GLY 3.3 0.6 - - - -
93A LYS* 1.3 77.2 - - - +
95A ALA* 1.3 62.2 + - - +
97A GLU* 3.4 3.0 + - - +
98A ILE* 2.9 36.9 + - + +
127A LEU* 6.0 0.2 - - + -
136A LEU* 5.0 1.3 - - + +
187A TRP* 3.9 16.2 - - + +
190A VAL* 4.0 12.3 - - + -
191A GLU* 3.5 46.3 - - + +
194A LEU* 3.9 13.7 - - + -
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Residues in contact with ALA 95 (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 PRO* 3.5 32.0 - - + +
91A THR* 3.4 11.7 + - - -
92A GLY 3.3 9.9 + - - +
94A VAL* 1.3 78.3 - - - +
96A ASP* 1.3 66.4 + - - +
98A ILE* 3.3 3.8 + - - +
99A ASN* 2.9 39.2 + - - +
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Residues in contact with ASP 96 (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 GLY* 3.0 24.1 + - - +
93A LYS* 3.5 22.6 + - + +
95A ALA* 1.3 78.6 - - - +
97A GLU* 1.3 58.8 + - + +
99A ASN* 3.4 8.8 + - - +
100A ALA* 3.0 29.7 + - - +
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Residues in contact with GLU 97 (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 LYS* 2.9 49.8 + - + +
94A VAL* 4.0 2.0 - - - +
96A ASP* 1.3 73.9 - - + +
98A ILE* 1.3 65.7 + - - +
100A ALA* 3.4 5.9 + - - +
101A SER* 3.1 27.9 + - - -
129A LYS* 3.1 38.5 + - - -
134A GLY 4.3 2.8 - - - +
136A LEU* 3.7 25.0 - - + +
194A LEU* 3.7 24.0 - - + +
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Residues in contact with ILE 98 (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 PRO* 4.0 14.1 - - + -
94A VAL* 2.9 37.8 + - + +
95A ALA* 3.8 4.7 - - - +
97A GLU* 1.3 77.4 - - - +
99A ASN* 1.3 58.0 + - - +
102A PHE* 2.9 38.7 + - + +
104A SER 4.1 1.1 - - - +
105A PHE* 4.0 20.9 - - + +
108A PHE* 3.7 39.7 - - + -
127A LEU* 4.5 9.4 - - + -
136A LEU* 3.9 17.3 - - + -
187A TRP* 4.1 13.5 - - + -
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Residues in contact with ASN 99 (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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95A ALA* 2.9 31.0 + - - +
96A ASP* 3.7 8.5 + - - +
98A ILE* 1.3 76.3 - - - +
100A ALA* 1.3 58.2 + - - +
103A GLY* 2.8 41.9 + - - +
104A SER* 3.6 3.5 - - - +
105A PHE* 3.5 24.3 + - - +
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Residues in contact with ALA 100 (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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96A ASP 3.0 17.9 + - - +
97A GLU* 3.8 7.9 - - - +
98A ILE 3.3 0.2 - - - -
99A ASN* 1.3 76.7 - - - +
101A SER* 1.3 61.4 + - - +
103A GLY 4.9 0.5 + - - -
135A LYS* 3.2 20.6 + - - +
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Residues in contact with SER 101 (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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97A GLU 3.1 15.2 + - - -
100A ALA* 1.3 79.4 - - - +
102A PHE* 1.3 68.9 + - - +
103A GLY 3.7 0.2 - - - -
134A GLY 4.7 0.9 + - - -
135A LYS* 3.6 21.0 + - - +
136A LEU* 2.7 51.3 + - - +
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Residues in contact with PHE 102 (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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98A ILE* 2.9 26.9 + - + +
101A SER* 1.3 82.6 - - - +
103A GLY* 1.3 57.9 + - - +
104A SER 3.3 18.1 + - - +
107A LYS* 3.4 21.3 - - + +
108A PHE* 3.6 43.3 - + + +
111A GLU* 3.6 25.8 - - - -
127A LEU* 3.8 7.9 - - + -
136A LEU* 3.7 39.5 - - + -
137A LYS* 3.8 12.3 - - - -
138A VAL* 3.9 19.7 - - + -
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Residues in contact with GLY 103 (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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99A ASN* 2.8 29.8 + - - +
100A ALA 4.6 0.6 + - - -
101A SER 3.7 0.8 - - - -
102A PHE* 1.3 75.1 - - - +
104A SER* 1.3 60.3 + - - +
107A LYS* 4.6 9.4 - - - -
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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