Contacts of the strand formed by residues 89 - 95 (chain A) in PDB entry 1G86
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 PHE 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ILE* 4.6 10.8 - - + -
23A LYS* 3.4 4.7 - - - +
24A GLY* 2.9 55.3 + - - +
25A ARG* 3.7 9.4 - - - -
26A PRO* 4.1 13.7 - - + -
36A LEU* 3.8 26.9 - - + -
58A PHE* 3.9 17.9 - + - -
83A PHE* 3.9 34.5 - + + -
84A GLN 6.1 1.6 - - - +
87A GLN 4.3 2.0 - - - +
88A GLU* 1.3 78.2 - - - +
90A GLU* 1.3 61.4 + - - +
91A LEU* 4.2 18.4 - - + -
104A VAL* 4.9 0.4 - - + -
105A ASN* 3.4 13.9 - - - +
130A ILE* 4.2 12.1 - - + -
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Residues in contact with GLU 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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21A THR* 4.1 22.9 - - + +
22A ILE 3.4 4.5 - - - +
23A LYS* 3.0 39.8 + - + +
89A PHE* 1.3 75.0 - - - +
91A LEU* 1.3 64.0 + - - +
92A SER* 4.1 3.8 + - - +
103A MET 3.7 0.9 - - - +
104A VAL* 3.5 4.2 - - - +
105A ASN* 2.8 49.7 + - - +
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Residues in contact with LEU 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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20A VAL 3.6 1.0 - - - +
21A THR* 3.4 4.0 - - - +
22A ILE* 2.7 67.5 + - + +
36A LEU* 4.4 12.8 - - + -
38A VAL* 4.2 11.4 - - + -
54A PHE* 4.0 20.2 - - + -
83A PHE* 4.1 13.0 - - + -
89A PHE* 4.1 10.5 - - + -
90A GLU* 1.3 75.3 - - - +
92A SER* 1.3 59.7 + - - +
93A ILE* 4.3 9.4 - - + -
102A VAL* 3.6 29.4 - - + -
103A MET 3.5 1.1 - - - +
104A VAL* 3.8 20.6 - - + -
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Residues in contact with SER 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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19A THR* 3.4 23.7 - - - +
20A VAL 3.3 4.0 - - - -
21A THR* 4.2 9.2 + - - -
90A GLU* 4.1 5.1 + - - -
91A LEU* 1.3 74.3 - - - +
93A ILE* 1.3 60.9 + - - +
94A SER* 4.0 3.5 + - - -
101A GLN 3.6 1.7 - - - +
102A VAL* 3.4 2.8 - - - -
103A MET* 2.7 57.5 + - - +
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Residues in contact with ILE 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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18A SER 4.0 0.5 - - - +
19A THR* 3.4 3.2 - - - -
20A VAL* 2.8 47.7 + - + +
22A ILE* 4.5 9.0 - - + -
38A VAL* 4.5 15.9 - - + -
40A PHE* 4.1 24.9 - - + -
52A PHE* 4.2 16.2 - - + -
54A PHE* 5.5 2.9 - - + -
91A LEU* 4.3 21.1 - - + -
92A SER* 1.3 77.2 + - - +
94A SER* 1.3 61.0 + - - +
95A VAL* 4.2 2.2 + - + +
100A TYR* 3.9 30.5 - - + -
101A GLN 3.5 4.0 - - - +
102A VAL* 4.2 20.0 - - + -
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Residues in contact with SER 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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18A SER 3.6 4.7 - - - -
19A THR* 3.3 20.0 + - - +
92A SER* 4.0 4.5 + - - -
93A ILE* 1.3 73.2 - - - +
95A VAL* 1.3 64.5 + - - +
96A LEU* 3.5 15.4 + - - -
100A TYR* 3.3 7.3 - - - -
101A GLN* 2.8 44.2 + - - +
103A MET* 5.6 4.3 - - - +
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Residues in contact with VAL 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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14A LEU* 4.3 16.6 - - + -
15A SER 3.5 20.6 - - - +
16A THR* 3.6 2.9 - - - +
17A GLY* 2.9 24.8 + - - -
18A SER* 2.9 29.2 + - - +
20A VAL* 5.9 1.3 - - + -
40A PHE* 5.6 0.4 - - + -
93A ILE* 5.0 2.9 - - + +
94A SER* 1.3 74.2 - - - +
96A LEU* 1.3 66.8 + - - +
99A LYS 4.2 1.3 - - - -
100A TYR* 4.0 19.5 - - + -
114A HIS* 3.8 9.9 - - + -
118A PRO* 3.6 32.3 - - + -
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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