Contacts of the strand formed by residues 232 - 236 (chain C) in PDB entry 3SAJ
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 VAL 232 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C LEU* 4.7 11.0 - - + -
210C TYR* 3.4 19.1 - - + +
212C LEU* 3.7 26.0 - - + -
217C PHE* 3.7 30.0 - - + -
225C PHE* 4.5 18.8 - - + -
230C ALA* 3.7 20.3 + - + -
231C ASN* 1.3 77.2 - - - +
233C THR* 1.3 67.8 + - - +
352C GLU* 3.7 1.0 - - - -
353C MET* 2.8 38.1 + - + +
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Residues in contact with THR 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ILE* 4.3 15.0 - - + -
122C TYR* 3.4 22.9 + - + -
210C TYR 2.8 14.9 + - - -
211C ILE* 3.5 14.1 - - + +
212C LEU* 2.9 30.0 + - - +
217C PHE* 4.3 2.5 - - - -
231C ASN 5.3 1.2 - - - -
232C VAL* 1.3 78.7 + - - +
234C GLY* 1.3 60.8 + - - +
350C VAL* 3.7 23.3 - - + -
351C ILE 3.2 11.7 - - - +
352C GLU* 4.2 4.9 - - - +
361C ILE* 4.2 9.2 - - + -
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Residues in contact with GLY 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C LEU* 4.5 9.0 - - - -
217C PHE* 3.5 23.2 - - - -
233C THR* 1.3 74.9 - - - +
235C PHE* 1.3 70.2 + - - -
350C VAL* 3.6 10.1 - - - +
351C ILE 3.0 31.1 + - - -
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Residues in contact with PHE 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C LEU* 4.3 20.4 - - + -
114C ALA* 3.6 31.4 - - + -
115C LEU* 3.9 18.4 - - + -
118C ILE* 3.9 28.3 - - + -
211C ILE* 5.4 2.7 - - + -
212C LEU 3.7 21.5 - - - -
213C ALA 5.0 1.8 - - - -
214C ASN 4.9 5.0 + - - -
215C LEU* 3.8 28.7 - - + +
216C GLY 5.0 0.3 + - - -
217C PHE* 3.9 20.6 + - - +
218C MET* 4.7 3.5 + - - +
234C GLY* 1.3 79.1 - - - -
236C GLN* 1.3 60.6 + - - +
348C LEU* 3.9 26.9 - - + -
349C HIS 3.4 7.2 - - - +
350C VAL* 4.6 8.3 - - + -
351C ILE* 4.8 2.2 - - - -
364C TRP* 5.2 0.9 - - + -
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Residues in contact with GLN 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C LEU* 4.9 0.4 - - - -
218C MET* 3.4 40.2 - - + +
235C PHE* 1.3 75.1 - - - +
237C LEU* 1.3 65.0 + - - +
238C VAL 3.4 26.4 + - - +
239C ASN* 3.9 12.7 + - - +
267C ARG* 4.4 2.9 + - - +
347C THR 4.8 0.2 - - - +
348C LEU* 4.1 3.3 - - - -
349C HIS* 2.9 41.6 + - + +
351C ILE* 3.9 19.6 - - + +
360C LYS* 3.8 29.8 - - - +
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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