Contacts of the helix formed by residues 173 - 182 (chain B) in PDB entry 3HS5
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LEU 3.6 2.4 + - - -
172B PRO* 1.3 71.3 - - - +
174B SER* 1.3 70.1 + - - +
175B LYS* 3.0 29.1 + - - +
176B GLU* 3.1 31.2 + - + +
177B VAL* 3.2 11.3 + - - +
449B LYS* 4.9 2.9 + - - -
456B ARG* 4.7 1.1 - - - +
494B LEU* 5.8 0.2 - - - +
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Residues in contact with SER 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B PRO 3.1 5.8 + - - -
173B ASP* 1.3 75.7 + - - +
175B LYS* 1.3 56.9 + - - +
177B VAL* 3.4 6.1 + - - +
178B LEU* 3.0 29.9 + - - +
449B LYS* 3.0 28.0 + - - +
452B ILE* 3.8 27.9 - - - +
453B ASP* 2.7 29.2 + - - -
456B ARG* 3.8 11.8 - - - +
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Residues in contact with LYS 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASP* 3.0 20.1 + - - +
174B SER* 1.3 80.8 + - - +
176B GLU* 1.3 63.4 + - - +
178B LEU* 3.5 6.4 + - + +
179B GLU* 2.6 74.4 + - + +
449B LYS* 4.2 23.7 - - + +
703B BOG 4.2 13.1 + - - -
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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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173B ASP* 3.1 29.6 + - + +
175B LYS* 1.3 82.2 - - + +
177B VAL* 1.3 64.7 + - - +
179B GLU* 4.7 12.9 - - - +
180B LYS* 3.0 57.2 + - - +
494B LEU* 4.0 21.8 - - + -
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B PRO* 3.8 21.1 - - + -
173B ASP 3.2 13.5 + - - +
174B SER* 3.4 6.5 + - - +
176B GLU* 1.3 74.9 - - - +
178B LEU* 1.3 64.7 + - - +
181B VAL* 3.1 40.0 + - + +
182B LEU* 3.8 1.9 + - + +
452B ILE* 4.1 11.0 - - + -
456B ARG* 4.4 7.2 - - - +
491B LEU* 4.9 1.1 - - + -
494B LEU* 4.0 11.4 - - + +
495B TYR* 3.5 34.3 - - + +
505B PRO* 3.9 22.7 - - + -
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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
----------------------------------------------------------
174B SER 3.0 17.1 + - - +
175B LYS* 3.6 10.5 - - + +
177B VAL* 1.3 77.7 - - - +
179B GLU* 1.3 61.4 + - + +
182B LEU* 3.1 25.6 + - + +
183B LEU* 3.0 51.8 + - + +
445B GLN* 3.8 35.0 - - + +
448B ALA* 3.6 31.6 - - + -
449B LYS* 4.1 21.8 - - + +
452B ILE* 4.5 3.1 - - + +
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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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175B LYS* 2.6 61.5 + - + +
176B GLU* 4.2 13.9 - - - +
178B LEU* 1.3 82.4 - - + +
180B LYS* 1.3 60.7 + - + +
183B LEU* 4.1 21.2 - - + +
185B ARG* 3.1 26.0 + - - -
445B GLN* 5.0 1.4 - - - +
703B BOG 3.3 49.0 + - + +
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Residues in contact with LYS 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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176B GLU* 3.0 41.2 + - - +
177B VAL 4.3 0.9 - - - +
179B GLU* 1.3 79.7 - - + +
181B VAL* 1.3 65.6 + - + +
185B ARG* 3.2 6.9 + - - +
438B ARG* 2.9 31.7 + - - -
490B GLU* 3.7 39.7 + - + +
494B LEU* 3.8 31.0 - - + -
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Residues in contact with VAL 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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177B VAL* 3.1 26.8 + - + +
180B LYS* 1.3 82.8 - - + +
182B LEU* 1.3 64.9 + - + +
437B GLY* 3.8 0.5 - - - -
438B ARG* 2.8 30.7 + - - +
487B MET* 3.9 36.9 - - + +
490B GLU* 4.1 11.9 - - + -
491B LEU* 3.9 28.3 - - + -
494B LEU* 5.6 0.9 - - + -
505B PRO* 5.6 0.4 - - + -
509B VAL* 3.6 27.3 - - + +
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Residues in contact with LEU 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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177B VAL* 4.1 3.8 - - + +
178B LEU* 3.1 29.3 + - + +
181B VAL* 1.3 83.3 - - + +
183B LEU* 1.3 62.3 + - - +
438B ARG* 3.7 2.0 - - - +
439B ASN 3.0 9.5 + - - -
440B VAL* 2.9 35.2 + - + +
448B ALA* 5.0 3.1 - - + -
452B ILE* 3.9 27.4 - - + -
504B TYR* 4.4 17.0 - - + -
505B PRO* 4.0 12.8 - - + +
508B LEU* 3.7 32.8 - - + +
509B VAL* 3.8 20.2 - - + -
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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