Contacts of the helix formed by residues 173 - 182 (chain A) in PDB entry 1CVU
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 ASP 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A LEU 3.6 2.0 + - - -
172A PRO* 1.3 72.3 - - - +
174A SER* 1.3 65.4 + - - +
175A LYS* 2.6 39.9 + - - +
176A GLU* 3.2 27.3 + - + +
177A VAL* 3.2 19.8 + - - +
449A LYS* 5.2 0.7 - - - -
456A ARG* 4.8 0.9 - - - +
494A LEU* 5.1 1.2 - - + +
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Residues in contact with SER 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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172A PRO 3.2 5.0 + - - -
173A ASP* 1.3 71.3 + - - +
175A LYS* 1.3 59.9 + - - +
177A VAL* 3.8 7.4 - - - +
178A LEU* 2.8 30.0 + - - +
449A LYS* 3.1 23.1 - - - +
452A ILE* 3.6 21.6 - - - +
453A ASP* 2.7 28.1 + - - -
456A ARG* 3.6 15.2 + - - +
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Residues in contact with LYS 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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173A ASP* 2.6 22.3 + - - +
174A SER* 1.3 76.3 + - - +
176A GLU* 1.3 57.6 + - + +
178A LEU* 3.3 10.6 - - + +
179A GLU* 2.9 66.4 + - + +
449A LYS* 4.2 16.5 - - + +
703A BOG 4.5 17.7 + - - -
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Residues in contact with GLU 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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173A ASP* 3.2 30.2 + - + +
175A LYS* 1.3 78.5 - - + +
177A VAL* 1.3 60.8 + - - +
179A GLU* 3.8 14.1 - - - +
180A LYS* 2.9 68.1 + - - +
494A LEU* 3.7 22.6 - - + +
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Residues in contact with VAL 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 PRO* 4.1 12.1 - - + +
173A ASP 3.2 16.8 + - - +
174A SER* 3.8 7.2 - - - +
176A GLU* 1.3 72.7 - - - +
178A LEU* 1.3 69.9 + - - +
181A VAL* 3.1 40.1 + - + +
182A LEU* 3.5 3.5 + - + +
452A ILE* 4.4 9.9 - - + -
456A ARG* 4.6 2.0 - - - +
491A LEU* 4.7 2.0 - - + -
494A LEU* 4.1 19.3 - - + -
495A TYR* 3.7 35.7 - - + +
505A PRO* 4.1 19.7 - - + -
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Residues in contact with LEU 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 2.8 20.4 + - - +
175A LYS* 3.3 11.9 - - + +
177A VAL* 1.3 76.3 - - - +
179A GLU* 1.3 60.8 + - + +
182A LEU* 2.7 47.3 + - + +
183A LEU* 2.8 32.6 + - + -
440A VAL* 5.1 0.4 - - + -
445A GLN* 3.7 40.4 - - + +
448A ALA* 4.0 20.2 - - + -
449A LYS* 4.5 22.2 - - + +
452A ILE* 4.5 1.5 - - + +
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Residues in contact with GLU 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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175A LYS* 2.9 49.8 + - + +
176A GLU* 3.8 16.0 - - - +
178A LEU* 1.3 74.8 - - + +
180A LYS* 1.3 55.4 + - + +
181A VAL 3.4 0.3 + - - -
183A LEU* 3.8 21.0 - - + +
185A ARG* 2.5 38.3 + - - -
445A GLN* 5.2 1.3 - - - +
703A BOG 3.0 57.4 + - + +
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Residues in contact with LYS 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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176A GLU* 2.9 60.1 + - - +
177A VAL 4.3 0.9 - - - +
179A GLU* 1.3 74.0 - - + +
181A VAL* 1.3 64.7 + - + +
185A ARG* 2.8 15.2 + - - +
438A ARG* 2.9 12.3 + - - -
490A GLU* 3.1 46.5 - - + +
494A LEU* 4.4 15.1 - - + +
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Residues in contact with VAL 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 VAL* 3.1 27.9 + - + +
180A LYS* 1.3 85.0 - - + +
182A LEU* 1.3 64.6 + - + +
438A ARG* 2.7 29.9 + - - +
487A MET* 3.6 38.4 - - + +
490A GLU* 3.7 13.7 - - + +
491A LEU* 3.9 25.6 - - + -
494A LEU* 5.7 1.3 - - + -
505A PRO* 6.0 0.2 - - + -
509A VAL* 3.6 22.9 - - + +
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Residues in contact with LEU 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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177A VAL* 3.8 11.9 - - + +
178A LEU* 2.7 34.6 + - + +
181A VAL* 1.3 86.5 - - + +
183A LEU* 1.3 64.5 + - - +
438A ARG* 3.5 1.6 - - - +
439A ASN 3.0 19.1 + - - -
440A VAL* 3.0 18.8 + - + +
448A ALA* 4.8 4.3 - - + -
452A ILE* 4.0 26.9 - - + -
504A TYR* 4.3 18.6 - - + -
505A PRO* 4.0 21.1 - - + +
508A LEU* 4.0 29.2 - - + +
509A VAL* 4.5 3.8 - - + -
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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