Contacts of the strand formed by residues 172 - 185 (chain A) in PDB entry 5C7Z
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 GLU 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A ARG* 2.7 52.5 + - + +
171A ASN* 1.3 76.5 - - - +
173A LEU* 1.3 57.6 + - - +
174A PHE* 3.5 28.2 - - + -
205A TYR* 2.7 50.1 + - + +
206A LEU* 4.0 3.9 - - - +
418A VAL* 4.3 0.7 - - - -
419A ILE* 3.2 21.4 - - + +
421A TRP* 2.8 22.5 + - + +
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Residues in contact with LEU 173 (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 GLU* 1.3 76.0 - - - +
174A PHE* 1.3 67.7 + - - +
175A LEU* 4.3 20.2 - - + -
202A MET* 4.0 11.9 - - + -
203A LYS 3.1 11.4 - - - +
204A SER* 4.0 9.2 - - - -
206A LEU* 4.2 5.8 - - + -
404A LEU* 3.7 35.9 - - + -
406A VAL* 4.0 9.6 - - + -
418A VAL* 3.9 19.5 - - + -
419A ILE 2.9 10.5 + - - +
420A LYS* 4.0 23.6 - - + -
421A TRP* 3.0 31.1 + - - +
5B ILE* 4.5 2.0 - - + -
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Residues in contact with PHE 174 (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 GLU* 3.5 39.0 - - + -
173A LEU* 1.3 76.6 - - - +
175A LEU* 1.3 64.0 + - - +
176A ASP* 4.2 0.9 + - - +
201A VAL 3.8 0.5 - - - +
202A MET* 3.5 4.0 - - - +
203A LYS* 2.8 56.0 + - + +
205A TYR* 4.1 22.9 - + - -
421A TRP* 3.3 35.2 - + + -
2B TYR* 3.7 39.5 - + + +
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Residues in contact with LEU 175 (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* 4.3 5.6 - - + -
174A PHE* 1.3 73.5 - - - +
176A ASP* 1.3 62.5 + - - +
177A VAL* 4.1 2.0 - - + -
200A VAL* 4.2 15.9 - - + -
201A VAL 3.5 2.7 - - - +
202A MET* 3.8 34.1 - - + -
214A PHE* 4.2 9.6 - - + -
274A LEU* 5.3 2.0 - - + -
401A VAL* 4.1 18.6 - - + -
404A LEU* 4.0 25.4 - - + -
421A TRP 2.8 13.8 + - - +
422A VAL* 3.2 9.2 - - + -
423A ARG 2.8 31.0 + - - +
2B TYR* 3.6 1.0 - - - -
5B ILE* 3.8 24.5 - - + -
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Residues in contact with ASP 176 (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 PHE 4.9 0.4 - - - -
175A LEU* 1.3 71.7 + - - +
177A VAL* 1.3 62.2 + - - +
178A LEU* 3.7 25.0 + - + +
199A ARG 3.6 1.2 - - - +
200A VAL* 3.3 4.6 - - - -
201A VAL* 2.9 37.8 + - + +
203A LYS* 2.9 28.3 + - - -
423A ARG* 2.9 30.4 + - + +
2B TYR* 2.4 29.7 + - - -
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Residues in contact with VAL 177 (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 LEU* 5.2 0.9 - - + -
176A ASP* 1.3 74.1 - - - +
178A LEU* 1.3 60.1 - - - +
179A GLU* 4.2 7.1 + - + +
199A ARG 3.6 4.0 - - - +
200A VAL* 4.6 13.9 - - + +
277A TYR* 3.4 25.8 - - - +
395A ALA* 4.3 6.4 - - + +
399A LEU* 4.2 13.7 - - + -
401A VAL* 4.1 18.8 - - + -
422A VAL* 4.3 4.9 - - + -
423A ARG 2.9 8.1 + - - +
424A TYR* 3.5 35.5 - - + -
425A ILE 3.0 24.9 + - - +
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Residues in contact with LEU 178 (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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176A ASP* 4.0 21.8 - - + +
177A VAL* 1.3 73.9 - - - +
179A GLU* 1.3 60.3 - - - +
197A SER 4.1 0.2 - - - +
198A GLY* 3.2 1.9 - - - -
199A ARG* 2.8 71.7 + - + +
201A VAL* 3.7 19.7 - - + -
423A ARG* 5.6 0.9 - - - +
425A ILE* 3.4 39.7 - - + +
427A ARG* 4.1 14.7 + - - +
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Residues in contact with GLU 179 (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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177A VAL* 4.1 4.9 + - + +
178A LEU* 1.3 76.7 - - - +
180A SER* 1.3 56.9 + - - +
181A VAL 4.0 0.2 - - - -
196A VAL* 3.7 15.3 - - + +
197A SER 3.3 4.9 - - - +
198A GLY* 3.9 6.3 - - - -
277A TYR* 2.4 32.2 + - - +
395A ALA* 3.1 16.6 - - + +
396A PRO* 3.0 37.0 - - + +
397A SER* 2.6 30.0 + - - -
399A LEU* 4.1 0.5 - - - +
425A ILE 3.1 6.4 + - - +
426A GLY* 3.3 2.8 - - - -
427A ARG* 2.7 39.6 + - - +
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Residues in contact with SER 180 (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 GLU* 1.3 74.3 - - - +
181A VAL* 1.3 59.2 + - - +
182A ASN* 3.4 17.8 + - - -
196A VAL* 3.4 3.5 - - - -
197A SER* 2.9 37.4 + - - -
427A ARG* 3.1 36.7 - - - +
428A SER 4.8 0.9 - - - -
429A GLY* 3.9 10.8 - - - -
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Residues in contact with VAL 181 (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 GLU 4.0 0.4 - - - -
180A SER* 1.3 73.2 + - - +
182A ASN* 1.3 69.3 + - - +
195A HIS 3.8 3.6 - - - +
196A VAL* 4.0 15.7 - - + -
283A ILE* 4.0 17.7 - - + -
284A ILE 4.8 1.6 - - - +
285A LEU* 4.5 5.2 - - + -
286A PRO* 4.4 2.5 - - + -
390A PHE* 3.9 26.9 - - + -
396A PRO* 3.8 30.1 - - + -
427A ARG 2.7 20.3 + - - +
429A GLY 3.0 17.5 + - - +
430A ILE 4.0 0.3 - - - +
431A TYR* 3.7 20.4 - - + -
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Residues in contact with ASN 182 (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 SER* 3.4 26.7 + - - -
181A VAL* 1.3 77.0 - - - +
183A LEU* 1.3 61.1 + - - +
193A SER 5.3 0.2 - - - -
194A ALA* 3.1 8.7 - - - +
195A HIS* 2.9 72.0 + - + +
197A SER* 4.3 2.4 + - - -
285A LEU* 5.0 0.2 - - - +
429A GLY* 3.2 6.1 - - - -
430A ILE* 2.9 43.0 + - + +
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Residues in contact with LEU 183 (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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182A ASN* 1.3 75.4 - - - +
184A LEU* 1.3 79.3 + - - +
185A MET* 4.2 21.3 - - + +
191A VAL* 4.3 10.3 - - + -
193A SER 3.4 10.8 - - - +
194A ALA* 4.2 4.7 - - + -
285A LEU* 3.8 34.8 - - + -
287A PHE 4.6 2.2 - - - +
430A ILE* 2.7 16.3 + - - +
431A TYR* 3.5 48.8 + - + +
432A GLU* 3.0 28.8 + - - +
433A THR* 5.1 3.8 - - - +
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Residues in contact with LEU 184 (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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183A LEU* 1.3 78.0 - - - +
185A MET* 1.3 62.3 + - - +
191A VAL 3.8 0.9 - - - -
192A LEU* 2.9 44.6 + - + +
193A SER* 2.8 31.0 + - - +
385A PRO* 5.3 1.3 - - + -
430A ILE* 6.0 1.6 - - + -
432A GLU* 3.5 29.8 - - + +
434A ARG* 4.1 38.6 - - + +
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Residues in contact with MET 185 (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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183A LEU* 4.2 22.4 - - + -
184A LEU* 1.3 74.0 - - - +
186A SER* 1.3 70.2 + - - +
189A GLY* 3.3 22.0 - - - +
190A GLN 3.1 23.1 - - - +
191A VAL* 3.8 17.9 - - + -
192A LEU* 4.1 2.2 - - - -
285A LEU* 4.4 7.4 - - + -
287A PHE 5.4 4.3 - - - +
288A ARG* 3.9 34.1 - - - +
289A VAL 5.8 0.4 - - - +
432A GLU 2.9 12.9 + - - +
433A THR* 4.0 16.2 - - + +
434A ARG* 2.9 35.6 + - - +
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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