Contacts of the helix formed by residues 90 - 99 (chain A) in PDB entry 1GNU
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 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A SER 3.4 13.6 + - - +
54A ASP* 4.3 15.7 - - + +
55A LEU 3.4 6.7 - - - -
56A THR* 4.2 5.6 - - + +
57A VAL* 4.7 1.6 - - - -
88A SER 4.7 4.3 - - - +
89A ALA* 1.3 77.7 - - - +
91A MET* 1.3 64.8 + - - +
92A GLY 3.6 1.4 + - - -
93A GLN* 3.0 47.3 + - - +
94A LEU* 3.0 19.6 + - - +
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Residues in contact with MET 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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29A VAL* 3.7 7.6 - - + +
31A VAL* 4.0 25.6 - - + -
51A VAL* 3.9 25.4 - - + -
52A PRO 4.0 5.6 - - - +
53A SER 3.5 0.2 + - - -
55A LEU* 2.8 33.6 + - + +
56A THR 4.5 0.9 - - - +
57A VAL* 4.2 19.1 - - - -
60A PHE* 3.9 36.1 - - + -
78A PHE* 6.3 0.4 - - - -
90A THR* 1.3 73.6 - - - +
92A GLY* 1.3 57.3 + - - +
94A LEU* 3.6 9.9 - - - +
95A TYR* 2.8 30.3 + - - +
105A LEU* 4.3 8.0 - - + +
107A ILE* 4.1 11.2 - - + -
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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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29A VAL* 3.8 14.4 - - - -
53A SER* 2.8 27.7 + - - +
90A THR* 4.0 0.7 - - - -
91A MET* 1.3 78.7 - - - +
93A GLN* 1.4 56.0 + - - +
95A TYR* 3.4 3.0 + - - +
96A GLN* 2.9 35.8 + - - +
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Residues in contact with GLN 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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88A SER 4.5 2.1 + - - +
89A ALA* 3.5 15.2 - - + +
90A THR* 3.0 55.2 + - - +
92A GLY* 1.4 72.4 - - - +
94A LEU* 1.3 66.7 + - - +
96A GLN* 3.2 10.2 + - - +
97A GLU* 3.1 26.9 + - - +
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Residues in contact with LEU 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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57A VAL* 4.0 23.6 - - + -
78A PHE* 6.5 0.2 - - + -
80A VAL* 4.2 20.6 - - + -
85A PRO* 4.1 24.0 - - + -
89A ALA* 5.4 4.8 - - + +
90A THR 3.0 11.1 + - - +
91A MET* 3.6 18.2 - - - +
93A GLN* 1.3 76.2 - - - +
95A TYR* 1.4 58.8 + - - +
97A GLU* 3.4 4.2 + - - +
98A HIS* 2.9 62.1 + - + +
105A LEU* 3.8 24.0 - - + -
107A ILE* 4.6 5.4 - - + -
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Residues in contact with TYR 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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22A ARG* 3.4 45.8 + - - +
29A VAL* 3.5 31.0 - - + -
30A PRO* 3.9 11.4 - - + -
91A MET 2.8 19.4 + - - +
92A GLY 3.6 4.9 - - - +
94A LEU* 1.4 76.9 - - - +
96A GLN* 1.3 70.1 + - + +
99A HIS* 2.9 55.6 + + + +
103A PHE* 2.7 45.8 + + - +
105A LEU* 4.0 21.9 - - + +
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Residues in contact with GLN 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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22A ARG* 5.3 9.4 - - - +
92A GLY 2.9 22.9 + - - +
93A GLN* 3.2 9.9 + - - +
95A TYR* 1.3 85.4 - - + +
97A GLU* 1.3 60.2 - - - +
99A HIS* 3.9 13.0 + - - -
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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 GLN 3.1 17.0 + - - +
94A LEU* 4.0 4.3 - - - +
96A GLN* 1.3 77.8 - - - +
98A HIS* 1.3 93.4 + - + +
99A HIS* 3.9 0.7 - - - -
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Residues in contact with HIS 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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80A VAL* 3.5 30.5 + - + +
81A ASN* 3.3 37.2 + - + +
83A VAL* 4.8 16.8 - - + +
94A LEU* 2.9 37.0 + - + +
97A GLU* 1.3 115.7 + - + +
99A HIS* 1.3 70.0 + - - +
100A GLU* 3.5 5.7 + - - +
105A LEU* 4.0 8.3 - - + +
106A TYR 5.4 0.9 + - - -
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Residues in contact with HIS 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 TYR* 2.9 64.2 + + + +
96A GLN* 3.9 13.5 + - - -
97A GLU 5.4 0.2 - - - -
98A HIS* 1.3 81.0 - - - +
100A GLU* 1.3 82.4 + - - +
101A GLU* 4.3 16.4 - - - +
103A PHE* 4.0 24.5 - + - -
104A PHE 3.7 9.0 - - - +
105A LEU* 4.2 4.4 - - - +
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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