Contacts of the helix formed by residues 175 - 185 (chain B) in PDB entry 1RGQ
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 175 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B ILE* 4.8 3.8 - - + -
99B PRO* 4.4 23.5 - - + +
100B CYS* 4.7 8.5 - - + +
153B ALA* 3.4 38.6 - - + +
154B VAL* 3.0 22.8 + - + +
155B GLY* 4.3 3.1 - - - +
156B LEU* 5.4 0.7 - - + -
173B ILE 4.0 0.6 + - - -
174B PRO* 1.3 70.8 - - - +
176B GLU* 1.3 71.5 + - - +
177B ASN 3.2 0.2 - - - -
178B LEU* 3.1 42.8 + - + +
179B GLU* 3.3 7.8 + - - +
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Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B CYS 5.7 0.5 - - - +
121B ARG* 4.1 12.0 + - - -
124B ASP* 5.1 6.4 - - - +
154B VAL* 4.4 1.4 - - - +
174B PRO* 3.2 29.7 - - + +
175B VAL* 1.3 84.4 + - - +
177B ASN* 1.3 64.9 + - - +
179B GLU* 3.5 7.3 + - - +
180B THR* 3.1 35.3 + - + +
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Residues in contact with ASN 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLN* 3.1 45.0 + - - +
85B LEU* 3.9 2.6 - - + +
173B ILE* 4.0 15.4 - - + +
174B PRO* 2.9 38.6 + - - +
176B GLU* 1.3 79.1 - - - +
178B LEU* 1.3 55.0 + - - +
180B THR* 3.5 7.0 + - - -
181B THR* 2.8 32.4 + - - -
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ILE* 3.9 35.0 - - + -
52B ASN* 5.8 2.0 - - - +
56B TRP* 3.7 37.8 - - + +
85B LEU* 3.6 37.5 - - + -
156B LEU* 4.1 15.0 - - + -
173B ILE* 5.1 1.8 - - + -
174B PRO 4.5 2.9 - - - +
175B VAL* 3.1 26.5 + - + +
177B ASN* 1.3 76.4 - - - +
179B GLU* 1.3 58.4 + - - +
181B THR* 3.0 18.9 + - - -
182B MET* 3.0 20.2 + - - +
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Residues in contact with GLU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ASN* 5.0 8.3 + - - +
175B VAL 3.3 8.2 + - - +
176B GLU* 3.5 9.1 + - - +
178B LEU* 1.3 78.6 - - - +
180B THR* 1.3 57.2 + - - +
182B MET* 3.4 22.0 + - - +
183B ARG* 3.1 61.6 + - - +
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Residues in contact with THR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLN* 4.1 12.6 + - - -
176B GLU* 3.1 18.6 + - + +
177B ASN* 3.5 12.8 + - - -
178B LEU 3.2 0.2 - - - -
179B GLU* 1.3 75.0 - - - +
181B THR* 1.3 61.5 + - - +
182B MET 3.3 0.2 - - - -
183B ARG* 3.4 33.3 - - - +
184B SER* 3.2 27.0 + - - -
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Residues in contact with THR 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B TRP* 4.3 9.0 - - + -
78B TYR* 3.7 34.7 - - + -
79B THR 4.9 1.6 - - - +
80B ASN* 2.9 42.7 + - + +
83B GLN* 3.3 1.9 + - - -
85B LEU* 3.7 10.7 - - + +
177B ASN 2.8 18.2 + - - -
178B LEU 3.0 10.5 + - - -
180B THR* 1.3 77.8 - - - +
182B MET* 1.3 62.4 + - - +
184B SER* 3.3 18.5 + - - +
185B GLY 4.3 3.8 + - - +
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Residues in contact with MET 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ASN* 4.6 22.0 - - + +
54B VAL* 3.9 23.3 - - + -
56B TRP* 3.9 18.2 - - + -
78B TYR* 3.5 42.9 + - + +
178B LEU* 3.0 16.3 + - - +
179B GLU* 3.6 30.1 - - - +
180B THR 3.3 0.2 - - - -
181B THR* 1.3 79.2 - - - +
183B ARG* 1.3 59.1 + - + +
184B SER 3.7 1.7 + - - -
185B GLY 5.0 0.7 + - - -
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Residues in contact with ARG 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B GLU* 3.1 51.9 + - - +
180B THR* 3.4 34.7 + - - +
181B THR 3.4 0.2 - - - -
182B MET* 1.3 76.7 - - + +
184B SER* 1.3 63.8 + - - +
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Residues in contact with SER 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ASN* 5.4 2.3 + - - -
180B THR 3.2 16.5 + - - -
181B THR* 3.3 17.0 + - - +
182B MET 3.5 1.8 - - - -
183B ARG* 1.3 80.5 - - - +
185B GLY* 1.3 65.7 + - - +
186B SER 4.1 10.9 + - - -
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Residues in contact with GLY 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B MET 5.1 6.2 - - - +
78B TYR* 5.3 7.8 - - - -
181B THR 4.3 4.3 + - - -
182B MET 5.0 1.4 + - - -
184B SER* 1.3 85.1 + - - +
186B SER* 1.3 61.0 + - - +
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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