Contacts of the strand formed by residues 195 - 202 (chain A) in PDB entry 4QA7
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 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A ILE* 3.7 35.7 - - + -
166A ARG* 4.0 17.9 - - + +
172A ILE* 3.3 15.3 - - + +
174A TYR* 4.9 1.3 - - + -
189A PHE* 3.8 41.7 - - + +
192A THR* 3.7 7.5 - - + +
193A SER 4.4 2.3 - - - -
194A LYS* 1.3 87.0 - - + +
196A MET* 1.3 63.8 + - - +
197A THR* 4.1 4.0 + - + -
225A TYR* 4.5 0.2 - - - +
255A PHE* 4.2 1.3 - - - -
403A K 2.7 28.4 - - - -
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Residues in contact with MET 196 (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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172A ILE 3.1 7.7 + - - +
173A LEU* 3.5 8.7 - - + +
174A TYR* 2.8 27.9 + - - +
195A VAL* 1.3 73.3 - - - +
197A THR* 1.3 69.0 + - - +
198A VAL* 4.4 0.9 - - + -
224A TYR 3.6 23.1 - - - +
225A TYR* 3.4 33.4 - - + +
226A SER 4.7 0.2 - - - +
227A VAL* 4.5 4.5 - - + -
251A VAL* 3.8 29.8 - - - -
255A PHE* 3.6 33.4 - - + -
373A LEU* 4.1 15.0 - - + -
376A VAL* 3.9 14.6 - - + -
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Residues in contact with THR 197 (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 TYR* 3.5 26.9 - - + -
185A VAL* 3.9 25.8 - - + +
186A GLU* 4.0 19.5 + - - +
189A PHE* 4.7 6.3 - - + -
195A VAL* 4.6 9.9 - - + +
196A MET* 1.3 77.9 - - - +
198A VAL* 1.3 59.4 + - - +
199A SER* 4.2 2.2 - - - -
225A TYR 3.3 3.6 + - - -
226A SER* 3.6 21.7 + - - -
227A VAL* 2.7 33.7 + - - +
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Residues in contact with VAL 198 (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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173A LEU* 3.9 23.8 - - + -
174A TYR* 2.6 13.5 + - - +
175A VAL* 3.4 7.9 - - + +
176A ASP* 2.7 34.6 + - - +
196A MET* 4.4 3.6 - - + -
197A THR* 1.3 78.7 - - - +
199A SER* 1.3 57.5 + - - +
200A LEU* 4.0 17.4 + - + -
227A VAL* 3.4 14.4 - - + -
229A VAL* 5.2 0.2 - - + -
247A VAL* 4.0 23.6 - - + -
248A LEU* 4.6 10.8 - - + -
251A VAL* 4.0 22.0 - - + -
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Residues in contact with SER 199 (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 TYR* 6.0 0.4 - - - -
176A ASP* 3.6 11.2 - - - -
181A HIS* 4.0 5.6 - - - -
182A GLY* 3.4 14.6 + - - -
186A GLU* 5.4 0.4 - - - -
197A THR* 5.7 2.0 - - - -
198A VAL* 1.3 74.3 - - - +
200A LEU* 1.3 61.2 + - - +
201A HIS* 2.8 26.9 + - - -
227A VAL 2.8 9.7 + - - +
228A ASN* 3.5 14.4 - - - -
229A VAL* 2.8 26.7 + - - +
402A K 3.0 15.2 - - - -
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Residues in contact with LEU 200 (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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175A VAL* 5.4 0.7 - - + -
176A ASP 3.0 10.1 + - - +
177A LEU* 4.1 15.3 - - + -
178A ASP 2.9 9.0 - - - +
198A VAL* 4.0 18.2 - - + -
199A SER* 1.3 76.1 - - - +
201A HIS* 1.3 60.3 + - - +
229A VAL* 3.8 26.2 - - + -
231A ILE* 4.2 14.8 - - + -
240A TYR* 3.7 33.7 + - + +
243A ILE* 4.6 7.2 - - + -
244A CYS* 3.9 40.2 - - + +
247A VAL* 5.4 3.4 - - + -
248A LEU* 6.1 0.9 - - + -
277A PHE* 5.1 2.2 - - - -
402A K 2.8 17.5 - - - -
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Residues in contact with HIS 201 (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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178A ASP 4.1 0.7 - - - -
179A LEU 3.3 15.5 - - - +
180A HIS 3.6 2.9 - - - -
181A HIS* 3.3 46.4 - + + +
199A SER* 2.8 27.6 + - - -
200A LEU* 1.3 73.7 - - - +
202A LYS* 1.3 73.8 + - - +
203A PHE* 4.3 5.8 - - + +
211A THR 4.2 3.4 - - - -
212A GLY* 2.6 33.8 + - - -
228A ASN* 3.4 13.5 - - + -
229A VAL 3.3 11.5 + - - +
230A PRO* 4.6 0.4 - - - +
231A ILE* 2.8 28.1 + - - +
277A PHE* 3.7 10.3 - - - -
402A K 3.8 0.7 - - - -
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Residues in contact with LYS 202 (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 LEU* 3.0 13.4 + - + +
181A HIS* 5.2 2.3 + - - +
201A HIS* 1.3 81.5 - - - +
203A PHE* 1.3 64.7 + - - +
204A SER* 4.3 13.2 - - - -
207A PHE* 3.6 59.5 - - + +
208A PHE 5.0 1.6 - - - +
209A PRO* 5.9 0.5 - - - +
211A THR 5.4 0.3 - - - +
231A ILE 3.2 11.0 - - - +
232A GLN* 5.3 1.8 - - - +
233A ASP* 3.2 33.2 + - - +
274A MET 5.5 0.2 + - - -
276A SER* 3.2 27.2 + - - +
277A PHE* 3.5 16.8 - - + -
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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