Contacts of the strand formed by residues 178 - 182 (chain A) in PDB entry 3P8P
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 CYS 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A LEU* 3.8 21.8 - - - -
174A LEU* 3.4 38.1 - - - -
175A LYS* 3.3 27.9 + - - +
177A PHE* 1.3 83.2 - - - +
179A SER* 1.3 69.4 + - - +
186A ILE* 4.3 6.3 - - + -
187A ALA 2.8 18.8 - - - +
188A ILE* 3.9 12.1 - - + -
201A MET* 4.5 5.6 - - + -
220A ALA* 3.6 5.2 - - - +
221A ASN* 4.2 0.2 - - - -
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Residues in contact with SER 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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132A LEU* 3.5 16.1 - - - +
175A LYS* 4.4 4.7 - - - -
178A CYS* 1.3 80.7 - - - +
180A MET* 1.3 63.0 + - - +
186A ILE* 3.5 2.3 - - - +
187A ALA* 2.6 36.7 + - - +
220A ALA 2.5 26.0 + - - -
221A ASN* 3.2 1.3 - - - -
222A CYS* 2.8 32.9 + - - -
273A THR* 4.4 10.8 - - - -
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Residues in contact with MET 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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10A PHE* 3.6 31.4 - - + -
132A LEU* 4.0 13.4 - - + +
133A PHE 3.8 11.9 - - - +
134A THR* 3.7 35.2 - - - +
179A SER* 1.3 76.8 - - - +
181A ALA* 1.3 57.0 + - - +
182A GLY 3.2 28.5 - - - +
184A ASN* 4.2 5.6 - - - +
185A LEU 3.4 17.0 - - - +
186A ILE* 3.7 23.1 - - + -
209A TYR* 4.9 1.1 - - + -
222A CYS* 4.0 9.2 - - - +
224A TYR* 3.3 21.9 + - + +
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Residues in contact with ALA 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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179A SER 3.4 1.4 + - - -
180A MET* 1.3 73.4 - - - +
182A GLY* 1.3 56.1 + - - +
185A LEU* 2.8 29.1 + - + +
187A ALA* 4.0 21.1 - - + +
212A LEU* 4.3 8.7 - - + -
222A CYS* 4.3 4.0 - - - -
224A TYR* 3.5 10.3 - - - +
234A LEU* 3.9 22.5 - - + +
255A HIS* 3.3 26.5 + - - -
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Residues in contact with GLY 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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10A PHE* 3.9 6.5 - - - -
180A MET* 3.2 17.9 - - - +
181A ALA* 1.3 82.6 - - - +
183A PRO* 1.3 73.6 - - - +
184A ASN 3.0 1.6 + - - -
185A LEU* 2.9 22.4 + - - -
224A TYR* 3.5 16.4 - - - -
255A HIS* 4.5 1.6 - - - -
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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