Contacts of the helix formed by residues 169 - 178 (chain A) in PDB entry 1S2C
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 ASN 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A ASN 3.9 0.8 + - - -
168A PHE* 1.3 75.8 - - - +
170A ARG* 1.3 63.7 + - - +
171A ARG* 3.2 10.9 + - - +
172A GLN* 2.9 44.6 + - - +
173A LEU* 3.0 21.5 + - - +
199A ARG* 5.3 7.4 - - - +
202A LEU* 4.3 8.1 - - - -
317A TYR 4.5 2.2 + - - -
318A PRO* 2.9 40.4 + - + +
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Residues in contact with ARG 170 (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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169A ASN* 1.3 74.7 - - - +
171A ARG* 1.3 58.0 + - - +
173A LEU* 3.3 6.4 + - - +
174A GLU* 2.9 32.6 + - - +
201A LYS* 3.7 40.7 - - - +
202A LEU* 3.6 35.6 - - + +
205A PHE* 3.8 29.3 - - + -
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Residues in contact with ARG 171 (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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169A ASN* 3.2 10.3 + - - +
170A ARG* 1.3 78.0 - - - +
172A GLN* 1.3 64.7 + - + +
174A GLU* 3.2 9.0 + - + +
175A MET* 3.0 37.5 + - + +
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Residues in contact with GLN 172 (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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119A PRO* 3.6 15.0 - - + +
144A LEU* 6.0 1.1 - - + -
168A PHE* 3.4 26.8 - - + -
169A ASN* 2.9 49.5 + - - +
171A ARG* 1.3 77.9 - - + +
173A LEU* 1.3 61.6 + - - +
175A MET* 3.4 23.2 + - - +
176A ILE* 3.6 16.3 + - - +
316A ASN* 3.0 50.8 + - - +
317A TYR 4.6 0.8 + - - -
318A PRO* 3.8 3.8 - - - +
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Residues in contact with LEU 173 (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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165A VAL* 3.6 30.7 - - + -
168A PHE* 4.0 6.4 - - + -
169A ASN 3.0 16.2 + - - +
170A ARG 3.6 4.3 - - - +
172A GLN* 1.3 75.1 - - - +
174A GLU* 1.3 65.5 + - - +
176A ILE* 3.1 9.1 + - + +
177A LEU* 3.1 25.8 + - + +
186A PRO* 4.1 19.7 - - + -
189A ASN* 4.1 15.0 - - + +
202A LEU* 4.8 2.0 - - + -
205A PHE* 3.9 15.7 - - + -
206A CYS* 3.9 28.5 - - - -
211A ILE* 3.9 24.0 - - + -
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Residues in contact with GLU 174 (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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170A ARG 2.9 14.8 + - - +
171A ARG* 3.4 10.3 - - + +
173A LEU* 1.3 77.1 - - - +
175A MET* 1.3 55.9 + - + +
177A LEU* 3.2 16.3 + - - +
178A ASN* 2.9 65.4 + - - +
205A PHE* 3.6 31.5 - - + -
209A LYS* 4.1 9.8 + - - -
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Residues in contact with MET 175 (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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143A ASP* 5.4 7.4 - - - +
144A LEU* 6.2 2.7 - - + +
145A CYS* 3.6 20.0 - - - -
171A ARG* 3.0 30.4 + - + +
172A GLN* 3.6 19.1 - - - +
173A LEU 3.2 0.4 - - - -
174A GLU* 1.3 77.4 - - + +
176A ILE* 1.3 61.0 + - + +
178A ASN* 3.6 5.7 + - - +
179A LYS* 3.4 14.6 + - - -
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Residues in contact with ILE 176 (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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116A ILE* 5.7 0.7 - - + -
144A LEU* 3.8 30.7 - - + +
145A CYS* 4.2 12.3 - - - -
148A TRP* 3.8 42.2 - - + +
165A VAL* 5.2 2.2 - - + -
168A PHE* 4.1 22.0 - - + -
172A GLN 3.7 13.9 - - - +
173A LEU* 3.1 7.7 + - + +
175A MET* 1.3 77.3 - - + +
177A LEU* 1.3 62.4 + - - +
179A LYS* 3.2 19.2 + - + +
182A LEU* 3.5 8.8 - - + +
186A PRO* 4.0 26.0 - - + -
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Residues in contact with LEU 177 (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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173A LEU* 3.1 19.3 + - + +
174A GLU* 3.2 24.0 + - - +
176A ILE* 1.3 75.7 - - - +
178A ASN* 1.3 61.1 + - - +
179A LYS 3.4 2.0 + - - +
182A LEU* 3.7 15.1 - - + +
185A LYS* 3.8 30.5 - - + -
186A PRO* 3.9 23.6 - - + -
205A PHE* 4.1 9.6 - - + -
209A LYS* 3.8 32.1 - - + -
211A ILE* 3.9 16.2 - - + -
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Residues in contact with ASN 178 (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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174A GLU* 2.9 50.7 + - - +
175A MET* 4.0 5.1 - - - +
176A ILE 3.2 0.2 - - - -
177A LEU* 1.3 78.2 - - - +
179A LYS* 1.3 66.9 + - - +
180A PRO* 3.2 8.5 - - - +
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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