Contacts of the strand formed by residues 187 - 195 (chain A) in PDB entry 3NGN
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
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Residue Dist Surf HB Arom Phob DC
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180A ARG* 3.6 2.0 - - - +
186A SER* 1.3 75.3 - - - +
188A SER* 1.3 62.4 + - - +
189A PHE* 4.0 3.9 - - + -
334A VAL* 4.9 5.4 - - + -
338A LEU* 3.4 31.4 - - + +
339A PHE* 3.6 25.6 - - + -
536A LEU 3.8 0.3 - - - +
537A GLU* 3.6 1.2 - - - -
538A LEU* 2.8 41.9 + - + +
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Residues in contact with SER 188 (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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180A ARG* 3.5 35.9 + - - +
187A ALA* 1.3 75.9 - - - +
189A PHE* 1.3 66.2 + - - +
234A ASP* 4.7 0.3 - - - +
291A LYS* 5.1 3.8 + - - -
338A LEU* 4.3 15.2 + - - +
501A LEU* 4.0 3.1 - - - -
535A GLN* 3.3 27.0 + - - -
536A LEU 3.1 10.1 - - - -
537A GLU* 4.3 0.9 - - - +
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Residues in contact with PHE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ALA* 4.0 7.6 - - + -
188A SER* 1.3 80.1 - - - +
190A THR* 1.3 67.0 + - - +
191A VAL* 3.6 27.8 + - + -
234A ASP* 3.3 19.3 - - + +
235A ILE* 4.1 11.0 - - + -
291A LYS* 5.7 0.2 - - + -
292A PHE* 4.4 15.5 - + + -
334A VAL* 6.2 2.2 - - + -
338A LEU* 5.3 4.9 - - + -
354A LEU* 4.1 25.6 - - + -
406A VAL* 4.3 4.3 - - + -
498A MET* 4.1 18.6 - - - -
535A GLN* 3.4 3.7 - - - +
536A LEU* 2.7 53.2 + - + -
538A LEU* 4.0 29.6 - - + -
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Residues in contact with THR 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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174A TRP* 4.9 7.0 - - + -
189A PHE* 1.3 78.1 - - - +
191A VAL* 1.3 65.3 - - - +
231A CYS 6.1 0.2 - - - +
232A ASP 4.1 3.1 + - - -
233A ALA* 3.4 11.1 - - - -
234A ASP* 2.9 35.4 + - - +
235A ILE* 3.0 26.2 + - - +
533A LEU* 4.3 12.8 - - + -
534A THR 3.1 12.8 - - - +
535A GLN* 3.9 18.8 - - + -
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Residues in contact with VAL 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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189A PHE* 3.6 26.0 - - + -
190A THR* 1.3 77.8 - - - +
192A MET* 1.3 64.2 + - - +
235A ILE* 3.3 21.1 - - + +
406A VAL* 4.1 16.8 - - + -
408A CYS* 3.7 30.7 - - - -
491A ILE* 3.6 10.2 - - + +
533A LEU* 3.2 6.0 - - - -
534A THR* 2.8 45.9 + - + -
536A LEU* 3.7 15.5 - - + -
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Residues in contact with MET 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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191A VAL* 1.3 78.2 - - - +
193A CYS* 1.3 60.8 + - - +
194A TYR* 3.8 13.7 - - + -
227A GLU* 3.7 20.6 - - + +
228A ILE* 4.0 14.1 - - - +
231A CYS* 3.6 28.0 - - + -
233A ALA* 3.6 17.8 - - + +
235A ILE 2.8 11.2 + - - +
236A ILE* 3.6 25.0 - - + -
237A SER* 2.8 31.5 + - - -
491A ILE* 4.4 0.2 - - - -
531A SER* 3.5 26.7 - - - -
532A LEU 3.2 12.6 - - - +
533A LEU* 3.9 8.1 - - + -
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Residues in contact with CYS 193 (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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192A MET* 1.3 73.8 - - - +
194A TYR* 1.3 61.4 + - - +
237A SER* 3.3 4.5 - - - -
239A GLN* 3.6 25.8 - - - -
408A CYS* 3.8 20.9 - - - -
409A ALA 3.9 8.7 - - - -
489A ASP* 4.9 7.9 - - - +
490A TYR 3.8 15.9 - - - -
491A ILE* 3.7 22.9 - - + +
530A PHE 4.6 1.4 - - - +
531A SER* 3.6 1.0 - - - -
532A LEU* 2.9 35.0 + - + +
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Residues in contact with TYR 194 (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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192A MET* 3.8 22.7 - - + -
193A CYS* 1.3 78.7 - - - +
195A ASN* 1.3 73.5 + - - +
196A VAL* 3.5 16.5 + - + -
224A ILE* 4.3 17.9 - - + +
227A GLU* 3.4 31.3 - - + +
228A ILE* 4.1 7.9 - - + -
237A SER 2.9 9.9 + - - -
238A LEU* 3.4 17.5 - - + +
239A GLN* 3.1 23.6 + - - +
525A ILE* 6.1 0.2 - - - +
526A PRO* 3.8 22.0 - - - +
527A SER* 3.7 16.7 - - - -
529A HIS 3.6 22.0 + - - -
530A PHE 4.2 2.2 - - - -
531A SER* 3.6 24.0 - - - +
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Residues in contact with ASN 195 (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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194A TYR* 1.3 77.6 - - - +
196A VAL* 1.3 53.5 + - - +
197A LEU* 3.0 17.5 + - - -
239A GLN* 3.3 20.9 + - - +
240A GLU* 3.0 39.0 + - - +
360A HIS* 3.8 4.0 - - - -
410A ASP* 2.8 25.7 + - - +
489A ASP* 4.3 4.4 + - - +
527A SER* 2.7 26.3 + - - -
528A ASP* 4.9 0.2 - - - +
529A HIS* 3.6 39.7 + - + +
556A AMP 3.7 0.2 + - - -
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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