Contacts of the helix formed by residues 171 - 176 (chain B) in PDB entry 1PH3
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 171 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A LYS 4.5 0.9 - - - +
396A LYS* 6.0 0.5 - - - +
412A GLN* 5.3 1.1 - - - +
169B LEU 3.0 6.4 + - - -
170B VAL* 1.3 75.4 - - - +
172B ILE* 1.3 72.7 + - - +
173B SER* 2.4 41.3 + - - +
174B LYS* 2.8 44.3 + - - +
175B VAL 3.9 0.9 + - - -
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Residues in contact with ILE 172 (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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390A TYR* 3.5 24.7 - - + -
395A LYS 3.5 18.4 - - - +
396A LYS* 4.3 0.9 - - - -
397A SER* 4.0 23.3 - - - +
410A ILE* 3.3 34.3 - - + -
412A GLN* 4.2 19.6 - - - +
434A TYR* 4.1 7.2 - - + -
436A GLN* 3.6 22.0 - - + +
170B VAL 3.1 7.0 + - - -
171B ASP* 1.3 75.3 + - - +
173B SER* 1.3 59.1 + - - +
175B VAL* 3.0 10.7 - - - +
176B ALA* 2.9 24.2 + - + +
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Residues in contact with SER 173 (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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395A LYS* 3.7 26.2 - - - -
171B ASP* 2.4 29.1 + - - +
172B ILE* 1.3 79.6 - - - +
174B LYS* 1.3 61.8 + - - +
176B ALA* 2.4 35.7 - - - +
181B LYS* 3.0 14.5 + - - -
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Residues in contact with LYS 174 (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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483A ASN* 3.2 40.6 + - - +
485A PHE* 4.2 15.7 - - + -
170B VAL* 4.0 21.5 - - + -
171B ASP* 2.8 33.1 + - + +
173B SER* 1.3 85.1 + - - +
175B VAL* 1.3 59.4 + - - +
178B ALA* 4.0 6.1 - - - +
181B LYS* 4.2 7.6 - - - +
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Residues in contact with VAL 175 (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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432A LEU* 3.8 26.2 - - + -
434A TYR* 3.3 28.7 - - + -
436A GLN* 4.3 11.2 + - - +
437A ASP* 4.3 1.0 - - - +
482A ARG* 3.1 39.3 + - - +
485A PHE* 4.4 11.0 - - + -
487A LEU* 3.9 21.8 - - + -
170B VAL* 4.3 9.2 - - + -
172B ILE* 3.0 17.2 - - + +
174B LYS* 1.3 79.4 - - - +
176B ALA* 1.3 60.4 + - - +
177B ASP 4.1 0.3 + - - -
178B ALA* 4.1 2.8 - - - +
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Residues in contact with ALA 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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390A TYR* 3.5 26.2 - - + +
395A LYS* 4.8 6.5 - - + +
436A GLN* 4.7 8.7 - - + -
437A ASP* 4.6 8.3 - - - +
172B ILE* 2.9 20.6 + - + +
173B SER* 2.4 30.6 - - - +
174B LYS 4.3 0.5 - - - -
175B VAL* 1.3 77.6 - - - +
177B ASP* 1.3 75.8 + - - +
178B ALA 3.3 1.3 - - - -
181B LYS* 3.3 0.9 + - - -
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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