Contacts of the strand formed by residues 187 - 192 (chain A) in PDB entry 6C3P
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 ALA 187 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A HIS* 1.3 74.8 - - - +
188A VAL* 1.3 58.2 + - - +
198A PHE* 3.4 25.8 - - + -
199A MET 3.2 18.6 - - - +
200A LEU* 3.9 9.2 - - + -
304A TYR* 4.1 14.7 - - + -
308A GLU 3.0 5.9 + - - -
309A ILE* 3.1 7.8 - - + +
310A LEU* 2.5 35.7 + - - +
315A PHE* 4.1 3.1 - - - -
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A HIS 5.3 0.2 - - - -
187A ALA* 1.3 78.0 - - - +
189A ILE* 1.3 62.8 + - - +
198A PHE* 4.8 0.2 - - - -
199A MET* 2.8 44.0 + - + +
310A LEU* 3.1 12.6 - - + +
313A GLN* 3.3 50.7 - - + +
314A ARG* 4.0 2.5 - - - -
315A PHE* 3.5 27.5 - - + -
336A THR* 3.6 24.0 - - + -
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Residues in contact with ILE 189 (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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188A VAL* 1.3 77.2 - - - +
190A ALA* 1.3 61.1 + - - +
196A LEU* 3.6 27.8 - - + -
197A CYS 3.1 26.5 - - - +
198A PHE* 3.8 18.2 - - + +
199A MET* 4.3 0.7 - - - -
261A ILE* 4.5 6.1 - - + -
270A LEU* 5.7 2.0 - - + -
275A LEU* 4.8 0.7 - - + -
309A ILE* 3.5 22.9 - - + +
310A LEU 3.1 26.9 + - - +
311A TRP* 3.6 35.2 - - + -
312A GLY* 3.3 7.8 + - - +
313A GLN 2.9 26.8 + - - +
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Residues in contact with ALA 190 (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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189A ILE* 1.3 79.6 - - - +
191A LEU* 1.3 65.7 + - - +
192A ARG 3.9 0.6 + - - -
195A ARG 3.6 0.2 - - - +
196A LEU* 3.3 15.5 - - - +
197A CYS* 3.0 30.8 + - - +
199A MET* 3.6 16.3 - - + +
312A GLY* 5.1 3.1 - - - -
313A GLN 3.4 14.1 - - - +
314A ARG* 3.6 18.8 - - + -
339A VAL* 6.1 3.6 - - + -
341A THR* 5.8 2.7 - - - -
229B GLU* 5.2 0.7 - - - +
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Residues in contact with LEU 191 (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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190A ALA* 1.3 78.5 - - - +
192A ARG* 1.3 61.3 + - - +
194A GLY* 4.5 6.1 - - - +
195A ARG* 3.5 24.7 - - - +
196A LEU* 3.7 19.5 - - + +
314A ARG* 5.4 1.6 - - - -
340A PRO 5.6 1.3 - - - +
341A THR* 4.2 12.6 - - - +
342A PRO* 4.1 25.4 - - + -
349A LEU* 5.6 7.4 - - + -
225B SER* 4.6 2.1 + - - -
227B GLU* 3.0 41.8 - - + +
229B GLU* 4.6 5.0 - - - +
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Residues in contact with ARG 192 (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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190A ALA 3.9 1.0 + - - -
191A LEU* 1.3 73.8 - - - +
193A HIS* 1.3 89.7 + - + +
194A GLY 3.2 0.9 - - - -
195A ARG* 2.6 38.9 + - - +
197A CYS* 3.6 18.2 - - - +
199A MET* 4.3 13.0 - - - -
256A ILE* 5.7 7.3 - - - +
258A TYR* 3.1 53.9 + - - -
260A VAL* 6.1 2.0 - - + +
225B SER* 4.2 12.0 - - - -
227B GLU* 3.2 4.0 + - - -
229B GLU* 3.1 31.8 + - - +
231B VAL* 5.2 11.5 - - - +
234B HIS* 4.6 17.2 + - - -
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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