Contacts of the helix formed by residues 162 - 171 (chain B) in PDB entry 1RQF
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 162 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B LEU* 4.6 5.6 - - - -
160B GLY* 3.3 0.8 - - - -
161B THR* 1.3 84.7 + - - +
163B PHE* 1.3 64.5 + - - +
164B PRO* 3.5 1.8 - - - -
165B HIS* 3.4 5.1 + - - +
166B MET* 3.0 24.4 + - - +
177D LYS* 4.3 20.6 - - - -
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Residues in contact with PHE 163 (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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88B ILE* 3.3 42.8 - - + -
89B LEU* 4.2 11.5 - - + +
94B ILE* 4.8 3.6 - - + -
97B MET* 3.5 47.6 - - + -
120B LEU* 4.1 12.8 - - + -
121B PRO* 3.4 34.3 - - + +
159B PHE 3.2 22.6 + - - +
160B GLY 4.2 0.6 + - - -
161B THR 3.6 0.4 - - - -
162B GLY* 1.3 76.3 - - - +
164B PRO* 1.3 77.3 - - + +
166B MET* 2.8 14.7 + - - +
167B LEU* 2.9 34.7 + - + +
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Residues in contact with PRO 164 (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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120B LEU* 4.1 13.9 - - + -
121B PRO 3.3 21.8 - - - +
122B ILE* 3.7 29.4 - - + -
136B TYR* 3.8 27.4 - - + -
161B THR 4.5 0.9 - - - +
162B GLY 3.8 1.1 - - - -
163B PHE* 1.3 101.8 - - + +
165B HIS* 1.3 68.4 + - + +
167B LEU* 3.5 4.9 + - + +
168B PHE* 3.1 32.2 + - + -
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Residues in contact with HIS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 4.6 8.1 - - + +
136B TYR* 3.8 35.8 - + - -
161B THR 4.0 11.4 + - - -
162B GLY* 3.9 5.6 - - - +
163B PHE 3.1 1.0 - - - -
164B PRO* 1.3 85.9 - - + +
166B MET* 1.3 65.3 + - - +
168B PHE* 3.6 5.2 + - - +
169B MET* 3.1 29.4 + - + +
139D LYS* 4.4 16.1 + - + +
141D MET* 4.9 12.4 - - + +
175D ARG* 6.0 2.5 - - + -
176D PRO 5.2 2.0 - - - +
177D LYS* 3.3 39.6 + - - +
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Residues in contact with MET 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 2.8 55.0 - - + +
91B ASN* 5.7 1.3 - - - +
94B ILE* 3.4 23.6 - - + -
162B GLY 3.0 11.9 + - - +
163B PHE* 2.8 10.2 + - + +
165B HIS* 1.3 77.7 - - - +
167B LEU* 1.3 63.6 + - - +
169B MET* 3.1 6.1 + - - +
170B VAL* 3.1 39.5 + - + +
175D ARG* 4.4 29.4 - - + +
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ILE* 4.1 24.1 - - + +
98B LEU* 4.1 43.3 - - + +
101B TYR* 5.4 1.8 - - + -
120B LEU* 4.3 14.4 - - + -
163B PHE* 2.9 37.3 + - + +
164B PRO* 3.7 7.9 - - + +
165B HIS 3.3 0.2 - - - -
166B MET* 1.3 77.7 - - - +
168B PHE* 1.3 91.2 + - + +
170B VAL* 3.3 1.2 + - - -
171B HIS* 2.8 34.1 + - + +
174B TYR* 5.2 0.7 - - + -
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Residues in contact with PHE 168 (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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101B TYR* 3.9 6.1 - + - -
120B LEU* 3.7 27.6 - - + -
136B TYR* 4.4 9.4 - + - -
138B PRO* 3.5 35.2 - - + -
164B PRO 3.1 25.9 + - - +
165B HIS* 3.6 1.8 + - - +
166B MET 3.3 0.2 - - - -
167B LEU* 1.3 88.7 - - + +
169B MET* 1.3 65.2 + - - +
171B HIS 3.7 6.3 - - - +
172B PRO* 3.0 24.9 - - - +
174B TYR* 3.5 27.1 - - + -
175B ARG* 3.9 21.1 - - + -
176B PRO* 4.5 0.4 - - + -
141D MET* 3.6 38.6 - - + +
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Residues in contact with MET 169 (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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165B HIS* 3.1 21.2 + - + +
166B MET* 3.1 8.8 + - - +
168B PHE* 1.3 75.9 - - - +
170B VAL* 1.3 60.3 + - + +
172B PRO* 3.0 22.1 - - - +
136D TYR* 4.2 18.2 - - - +
138D PRO 4.7 11.7 - - - +
141D MET* 4.8 7.2 - - - +
164D PRO 5.4 0.2 - - - +
165D HIS* 3.5 19.9 + - + -
168D PHE* 3.4 48.0 - - + -
175D ARG* 3.3 41.7 - - + +
176D PRO* 5.3 3.1 - - + -
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASN* 3.9 22.9 - - + +
94B ILE* 3.8 21.3 - - + -
166B MET* 3.1 27.8 + - + +
167B LEU 3.8 3.4 - - - +
169B MET* 1.3 79.3 - - + +
171B HIS* 1.3 82.2 + - + +
172B PRO* 3.3 4.6 - - - +
173B GLU* 4.4 1.2 - - - +
165D HIS* 5.1 3.9 + - - -
175D ARG* 6.1 2.2 - - - +
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Residues in contact with HIS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASN 5.6 1.0 + - - -
94B ILE* 3.7 24.2 - - + +
95B ALA* 5.0 6.9 - - + +
98B LEU* 3.7 29.3 - - + +
167B LEU* 2.8 18.0 + - + +
168B PHE* 3.4 9.3 - - - +
169B MET 3.3 0.2 - - - -
170B VAL* 1.3 108.5 + - + +
172B PRO* 1.3 66.0 - - - +
173B GLU* 2.9 27.7 + - - +
174B TYR* 2.9 27.0 + - + +
175B ARG 4.2 0.7 + - - -
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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