Contacts of the strand formed by residues 297 - 300 (chain V) in PDB entry 1O18
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 ASN 297 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151V ILE* 3.4 19.9 + - - +
152V VAL 5.6 0.2 - - - -
153V LEU* 4.5 13.5 - - - +
278V THR* 3.2 35.0 + - - +
282V ILE* 4.6 1.9 - - - +
293V LEU 3.7 3.3 + - - +
294V TYR* 5.0 2.3 - - - +
296V ASN* 1.3 70.9 - - - +
298V VAL* 1.3 62.0 + - - +
299V MET* 3.8 2.7 + - - -
313V MET* 4.4 12.9 - - - +
317V ILE* 3.9 9.2 - - - +
328V LYS 2.9 14.7 + - - +
329V ILE* 3.5 26.0 - - + +
330V ILE* 2.7 30.9 + - - +
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Residues in contact with VAL 298 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637G LYS* 3.6 22.7 - - - +
141V SER* 4.5 4.0 - - - +
142V LEU* 3.7 25.6 - - + -
145V SER* 3.5 21.1 - - - +
147V ARG* 4.3 9.4 - - - -
151V ILE 2.9 6.9 + - - +
152V VAL* 3.1 21.0 - - + +
153V LEU* 2.9 25.6 + - - +
296V ASN 4.4 3.1 - - - +
297V ASN* 1.3 75.4 - - - +
299V MET* 1.3 72.4 + - - +
300V SER* 5.3 0.2 - - - -
330V ILE* 3.3 17.7 - - + +
332V PRO* 5.3 4.0 - - + -
338V SER* 5.9 0.4 - - - +
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Residues in contact with MET 299 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153V LEU* 3.6 35.9 - - + -
297V ASN* 4.8 5.6 - - - -
298V VAL* 1.3 77.9 - - - +
300V SER* 1.3 63.9 + - - +
304V THR* 3.8 17.9 - - - +
309V ILE* 4.3 15.0 - - + -
310V ALA* 4.0 15.0 - - + -
313V MET* 4.8 11.0 - - - -
329V ILE* 3.6 31.6 - - + -
330V ILE 2.8 10.9 + - - +
331V ALA* 3.4 28.5 - - + -
332V PRO* 4.0 11.6 - - - +
335V ARG* 3.8 13.7 - - - +
338V SER* 4.4 1.4 + - - -
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Residues in contact with SER 300 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141V SER* 3.0 34.4 + - - -
152V VAL* 3.6 4.8 - - - +
153V LEU 3.1 9.9 + - - +
154V ASP* 3.0 23.5 + - - +
155V SER 3.1 21.3 + - - -
298V VAL* 4.2 0.6 + - - -
299V MET* 1.3 77.6 - - - +
301V GLY* 1.3 61.5 + - - +
304V THR* 3.3 10.7 - - - +
335V ARG* 4.0 4.9 - - - -
338V SER* 3.7 14.6 - - - -
339V VAL* 5.0 1.8 - - - -
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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