Contacts of the helix formed by residues 174 - 182 (chain A) in PDB entry 1I4W
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 SER 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A MET 3.3 1.6 + - - -
173A PRO* 1.3 69.5 - - - +
175A THR* 1.3 66.2 + - - +
177A ALA* 3.1 10.0 + - - +
178A ARG* 2.7 35.4 + - - +
207A ILE* 4.0 25.8 - - - -
212A GLU* 3.2 31.5 + - - -
216A PHE* 5.1 0.2 - - - -
241A PRO* 2.9 27.9 + - - +
242A ILE* 4.1 0.2 - - - +
243A ALA* 4.1 6.1 - - - -
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Residues in contact with THR 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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144A GLU* 4.2 9.1 + - - -
173A PRO* 4.0 10.7 - - + +
174A SER* 1.3 84.9 + - - +
176A THR* 1.3 69.8 + - - +
178A ARG* 3.4 17.9 + - - +
179A LYS* 3.4 28.6 + - - +
212A GLU* 5.2 5.4 - - - +
240A LYS* 5.4 13.2 - - + -
241A PRO* 6.2 0.2 - - + -
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Residues in contact with THR 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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143A SER* 3.2 22.1 + - - +
144A GLU* 3.2 29.6 + - + +
147A ILE* 4.3 20.9 - - + -
172A MET* 3.7 20.0 - - + -
173A PRO* 3.0 20.5 + - - +
175A THR* 1.3 82.4 + - - +
177A ALA* 1.3 57.9 + - - +
179A LYS* 3.4 4.9 + - - +
180A LEU* 3.0 28.5 + - + +
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Residues in contact with ALA 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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172A MET* 3.8 18.4 - - - -
173A PRO 3.0 12.2 + - - +
174A SER 3.1 7.8 + - - +
176A THR* 1.3 78.6 - - - +
178A ARG* 1.3 56.9 + - - +
180A LEU* 4.2 4.0 - - - -
181A LEU* 3.0 26.7 + - + +
204A LEU* 5.4 0.2 - - + -
216A PHE* 3.3 23.7 - - + -
243A ALA* 3.9 19.1 - - + -
245A VAL* 4.6 10.1 - - + -
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Residues in contact with ARG 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 SER 2.7 27.4 + - - +
175A THR* 3.7 15.7 + - - +
176A THR 3.2 0.2 - - - -
177A ALA* 1.3 76.5 - - - +
179A LYS* 1.3 62.8 + - - +
181A LEU 4.0 0.3 - - - -
182A ALA* 3.1 23.9 + - - +
186A MET* 5.2 0.3 - - - +
188A SER* 3.3 30.0 + - - -
212A GLU* 3.6 23.1 + - - -
215A GLY* 3.4 33.8 + - - +
216A PHE* 3.3 33.0 - - + -
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Residues in contact with LYS 179 (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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144A GLU* 3.1 40.1 + - - +
175A THR* 3.4 13.2 + - - +
176A THR* 3.9 6.5 - - - +
177A ALA 3.4 0.2 - - - -
178A ARG* 1.3 77.5 - - + +
180A LEU* 1.3 64.6 + - - +
182A ALA* 3.2 6.1 + - - +
188A SER* 3.6 26.2 - - - +
190A SER* 4.4 11.0 - - - +
192A CYS* 4.1 15.0 - - - -
193A SER* 2.8 26.3 + - - -
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Residues in contact with LEU 180 (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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147A ILE* 4.5 10.3 - - + -
151A LEU* 4.4 11.7 - - + -
172A MET* 4.1 29.8 - - + -
176A THR* 3.0 16.8 + - + +
177A ALA* 3.7 3.6 - - - +
179A LYS* 1.3 80.2 - - - +
181A LEU* 1.3 70.8 + - + +
192A CYS* 4.0 17.2 - - + +
193A SER* 3.3 13.0 - - - -
196A ARG* 2.9 57.4 + - + -
202A THR* 5.1 0.2 - - - +
245A VAL* 4.8 7.9 - - + -
247A MET* 4.2 21.1 - - + -
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Residues in contact with LEU 181 (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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177A ALA 3.0 13.7 + - - +
178A ARG 4.0 0.2 - - - -
180A LEU* 1.3 86.8 - - + +
182A ALA* 1.3 64.5 + - - +
183A ARG* 2.6 30.1 + - - +
186A MET* 5.4 0.2 - - - +
196A ARG* 3.9 4.0 - - - +
202A THR* 3.2 42.8 - - - +
204A LEU* 3.9 20.4 - - + +
216A PHE* 3.6 27.6 - - + -
217A ASP* 5.7 2.1 + - - +
224A TRP* 3.6 30.8 - - + -
245A VAL* 4.4 9.9 - - + -
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Residues in contact with ALA 182 (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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178A ARG 3.1 17.1 + - - +
179A LYS 3.2 17.5 + - - +
181A LEU* 1.3 75.7 - - - +
183A ARG* 1.3 61.4 + - - +
186A MET* 4.3 10.3 - - + -
188A SER* 3.5 7.9 - - - +
189A ARG* 2.9 51.6 + - - +
193A SER* 3.4 2.0 - - - +
196A ARG* 3.0 10.9 + - - -
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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