Contacts of the helix formed by residues 88 - 100 (chain R) in PDB entry 5A31
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 GLY 88 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1242A GLU* 5.6 7.2 + - - -
1244A ASP* 3.8 27.5 + - - -
89R LEU* 1.3 66.2 - - - +
90R ALA 3.4 2.5 - - - -
91R TYR* 3.7 8.3 + - - +
92R SER* 3.3 23.2 + - - -
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Residues in contact with LEU 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88R GLY* 1.3 77.8 - - - +
90R ALA* 1.3 58.3 + - - +
92R SER* 3.7 6.0 + - - -
93R ALA* 3.2 28.7 + - + +
107R VAL* 3.9 20.2 - - + -
108R GLN* 4.2 35.2 - - - +
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Residues in contact with ALA 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1241A THR 3.7 22.9 - - - +
1242A GLU* 4.2 10.5 - - + +
1243A LEU* 5.0 3.4 - - + -
88R GLY 3.4 0.4 - - - -
89R LEU* 1.3 79.3 - - - +
91R TYR* 1.3 60.9 + - - +
93R ALA* 3.8 3.3 + - - +
94R LEU* 3.2 26.7 + - - +
107R VAL* 4.5 14.0 - - + +
160R LEU* 4.2 15.7 - - + +
161R LEU* 5.7 2.6 - - + +
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Residues in contact with TYR 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197A LEU* 4.0 17.4 + - - +
1198A THR* 5.1 3.8 - - - -
1200A GLY* 5.7 5.2 - - - -
1205A SER* 5.0 2.8 + - - -
1230A ILE* 3.5 24.7 - - + -
1231A HIS* 3.0 36.3 + + - -
1242A GLU 5.2 0.2 + - - -
1243A LEU* 4.2 23.1 - - + +
1244A ASP* 4.5 21.5 - - - +
1245A VAL* 4.8 14.8 - - + -
88R GLY* 3.7 10.0 + - - +
89R LEU 3.4 0.2 - - - -
90R ALA* 1.3 78.8 - - - +
92R SER* 1.3 68.9 + - - +
94R LEU* 3.2 6.1 + - - +
95R LEU* 3.1 43.9 + - + +
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Residues in contact with SER 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1198A THR* 4.7 16.1 - - - +
88R GLY 3.3 15.7 + - - -
89R LEU* 3.8 7.4 - - - -
91R TYR* 1.3 83.9 - - - +
93R ALA* 1.3 67.6 + - - +
95R LEU* 3.0 18.6 + - - +
96R LYS* 3.2 25.2 + - - +
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Residues in contact with ALA 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89R LEU* 3.2 18.6 + - + +
90R ALA* 3.8 6.5 - - - +
92R SER* 1.3 80.1 + - - +
94R LEU* 1.3 55.5 + - - +
96R LYS* 3.3 26.1 + - - +
97R ASN* 2.4 27.1 + - - +
104R ILE* 4.4 20.0 - - + +
106R LYS 5.3 0.2 - - - +
107R VAL* 4.9 11.2 - - + -
160R LEU* 4.5 7.4 - - + -
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Residues in contact with LEU 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230A ILE* 3.4 26.2 - - + -
1236A LEU* 4.0 5.6 - - + -
1243A LEU* 3.8 11.7 - - + -
90R ALA 3.2 11.7 + - - +
91R TYR 3.4 9.6 - - - +
92R SER 3.2 0.8 - - - -
93R ALA* 1.3 79.0 - - - +
95R LEU* 1.3 61.1 + - - +
97R ASN* 3.2 6.5 + - - +
98R GLU* 3.1 40.8 + - - +
153R VAL* 4.2 2.0 - - + -
157R SER* 3.6 22.9 - - - -
160R LEU* 3.8 13.2 - - + +
161R LEU* 3.4 32.1 - - + -
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Residues in contact with LEU 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1194A HIS* 4.3 2.5 - - + +
1197A LEU* 3.7 23.8 - - + -
1198A THR* 3.8 22.4 - - + +
1227A LEU* 3.7 29.6 - - + -
1230A ILE* 4.5 11.4 - - + -
1231A HIS* 4.8 0.9 - - + -
91R TYR* 3.1 47.0 + - + +
92R SER* 3.0 11.6 + - - +
94R LEU* 1.3 73.9 - - - +
96R LYS* 1.3 65.0 + - - +
98R GLU* 3.0 15.2 + - + +
99R LEU* 3.2 33.4 + - + +
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Residues in contact with LYS 96 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1194A HIS* 3.5 24.2 - - + +
63R ARG* 4.0 17.7 - - + +
66R GLU* 4.6 15.5 - - - +
92R SER* 3.2 20.5 + - - +
93R ALA* 3.3 19.6 + - - +
95R LEU* 1.3 76.7 - - - +
97R ASN* 1.3 61.8 + - - +
100R LEU* 3.1 43.7 + - + +
102R ALA* 3.8 7.6 + - + -
104R ILE* 3.5 32.4 - - + +
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Residues in contact with ASN 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1226A ARG* 5.1 3.1 + - - -
93R ALA 2.4 32.4 - - - +
94R LEU* 3.2 7.2 + - - +
96R LYS* 1.3 75.4 - - - +
98R GLU* 1.3 65.8 + - - +
101R GLY* 4.0 14.9 + - - -
102R ALA 3.1 24.2 + - - +
103R GLY* 4.3 1.0 - - - -
104R ILE* 3.3 35.2 + - - +
154R SER* 5.5 2.6 + - - +
156R LYS* 4.3 1.4 - - + +
157R SER* 3.9 33.0 - - - +
160R LEU* 4.0 7.5 - - - +
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Residues in contact with GLU 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1223A SER 5.1 4.3 - - - +
1226A ARG* 3.4 53.2 + - + +
1227A LEU* 4.8 7.4 - - - +
1230A ILE* 3.9 14.0 - - + +
94R LEU* 3.1 32.7 - - + +
95R LEU* 3.0 13.1 + - + +
97R ASN* 1.3 80.0 - - - +
99R LEU* 1.3 65.5 + - + +
100R LEU 3.8 0.2 - - - -
101R GLY 5.2 0.2 - - - -
153R VAL* 3.1 47.1 - - - +
154R SER* 4.2 1.7 + - - -
157R SER* 3.9 2.6 + - - -
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Residues in contact with LEU 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190A THR* 3.7 33.3 + - - +
1193A ILE* 3.9 28.7 - - + -
1194A HIS* 3.4 38.4 - - + +
1197A LEU* 4.3 3.6 - - + -
1223A SER 6.0 1.1 - - - +
1227A LEU* 3.9 25.1 - - + -
59R VAL* 5.6 0.7 - - - +
95R LEU* 3.2 28.1 + - + +
98R GLU* 1.3 82.4 - - + +
100R LEU* 1.3 72.3 + - - +
101R GLY 3.9 0.9 - - - +
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Residues in contact with LEU 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1191A LEU* 4.3 20.4 - - + -
1194A HIS* 3.7 50.5 - - + +
56R ASN* 5.4 2.8 + - - -
59R VAL* 3.7 36.1 - - + +
60R ASN* 5.3 1.9 + - - -
62R HIS* 5.0 4.9 - - + -
63R ARG* 4.1 30.8 + - + +
96R LYS* 3.1 27.1 + - + +
99R LEU* 1.3 91.6 - - - +
101R GLY* 1.3 67.6 + - - +
102R ALA* 3.1 6.1 + - + +
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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