Contacts of the strand formed by residues 187 - 195 (chain A) in PDB entry 5NRO
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 ASN 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A GLY* 1.3 72.9 - - - -
188A ARG* 1.3 72.9 + - - +
189A THR* 4.8 4.0 + - - -
206A GLU* 2.8 35.5 - - - +
207A ILE 3.4 3.1 - - - -
208A ASP* 4.0 18.4 - - - +
335A ASP* 4.6 8.2 + - - +
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Residues in contact with ARG 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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179A TYR* 5.0 13.9 - - - -
183A LYS* 3.2 38.0 - - - +
184A GLY 2.8 31.9 + - - +
185A THR 4.4 5.9 + - - -
186A GLY* 3.7 21.5 + - - -
187A ASN* 1.3 78.8 - - - +
189A THR* 1.3 62.7 + - - +
190A ILE* 4.3 11.9 - - + -
206A GLU* 3.3 9.6 - - - +
207A ILE* 2.9 57.1 + - + +
209A GLU* 5.9 0.2 - - - +
214A LYS* 5.4 1.6 - - - +
335A ASP* 4.1 14.6 - - + -
336A ASP* 5.2 5.8 - - + +
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Residues in contact with THR 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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187A ASN* 4.8 4.3 + - - -
188A ARG* 1.3 78.4 + - - +
190A ILE* 1.3 65.1 + - - +
204A ILE* 4.1 7.4 - - + -
205A ILE 3.6 10.5 - - - +
206A GLU* 4.1 8.6 - - - +
219A LEU* 4.0 14.3 - - + +
329A LEU* 3.8 28.4 - - + +
333A ASP 3.8 15.8 + - - -
334A ILE* 4.3 5.4 - - + -
335A ASP* 2.7 39.1 + - - +
336A ASP 3.0 7.3 + - - -
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Residues in contact with ILE 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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176A ALA* 4.1 14.4 - - + -
179A TYR* 4.2 19.5 - - + -
188A ARG* 4.5 10.8 - - + -
189A THR* 1.3 82.4 - - - +
191A ALA* 1.3 60.2 + - - +
192A VAL* 3.8 22.7 - - + -
203A SER 3.6 0.5 - - - +
204A ILE* 3.4 5.4 - - - +
205A ILE* 2.9 48.3 + - + +
207A ILE* 4.0 23.8 - - + -
334A ILE* 4.3 4.3 - - - -
336A ASP* 3.0 26.7 - - + +
338A ILE* 4.3 13.0 - - + -
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Residues in contact with ALA 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 ILE* 1.3 72.7 - - - +
192A VAL* 1.3 61.4 + - - +
193A TYR* 3.9 0.4 - - + -
202A ILE* 4.2 5.6 - - + -
203A SER 3.5 4.9 - - - -
204A ILE* 3.6 20.2 - - + -
334A ILE* 3.9 8.7 - - + +
336A ASP 2.9 9.2 + - - +
337A VAL* 3.3 6.6 - - + +
338A ILE* 2.9 29.0 + - - +
357A PHE* 3.8 30.7 - - + -
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Residues in contact with VAL 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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172A PRO* 3.6 45.4 - - + +
175A ALA* 4.6 1.1 - - + -
176A ALA* 4.5 1.6 - - + -
190A ILE* 3.8 19.1 - - + -
191A ALA* 1.3 72.3 - - - +
193A TYR* 1.3 62.2 + - - +
194A ASP* 4.8 1.1 - - + +
201A ASP 3.7 1.7 - - - +
202A ILE* 3.2 10.1 - - - +
203A SER 2.9 35.6 + - - +
205A ILE* 4.3 6.5 - - + -
338A ILE* 3.7 25.1 - - + -
340A VAL* 4.2 23.3 - - + -
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Residues in contact with TYR 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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191A ALA 3.9 0.2 + - - -
192A VAL* 1.3 71.6 - - - +
194A ASP* 1.3 60.5 + - - +
195A LEU* 3.9 22.9 - - + +
200A PHE* 3.3 26.0 - + - -
201A ASP 3.8 1.8 - - - -
202A ILE* 4.5 3.6 - - + -
313A VAL* 5.2 2.4 - - - +
316A SER* 2.8 28.0 + - - -
317A ILE* 5.0 0.8 - - + +
320A LEU* 4.0 24.9 - - + -
337A VAL* 5.1 5.2 - - + -
338A ILE 3.0 15.5 + - - +
339A LEU* 3.5 21.4 - - + -
340A VAL* 2.9 26.3 + - - +
344A THR* 3.9 5.6 - - + -
349A VAL* 3.7 28.9 - - + +
353A VAL* 3.6 27.8 - - + +
357A PHE* 5.6 1.3 - + + -
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Residues in contact with ASP 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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171A GLU* 3.5 32.6 - - - +
172A PRO* 4.4 11.6 - - + +
192A VAL* 4.9 2.5 - - + -
193A TYR* 1.3 72.7 - - - +
195A LEU* 1.3 62.6 + - - +
196A GLY* 3.8 11.0 + - - -
199A ALA 4.9 1.2 - - - +
200A PHE* 3.1 10.1 - - - -
201A ASP* 2.9 51.8 + - + +
340A VAL* 3.2 33.5 - - + +
341A GLY* 4.1 2.4 - - - -
371A VAL* 4.5 2.3 - - - +
700A ATP 4.6 4.5 + - - -
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Residues in contact with LEU 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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193A TYR* 3.9 22.7 - - + +
194A ASP* 1.3 73.4 - - - +
196A GLY* 1.3 59.3 + - - +
199A ALA 3.8 0.4 - - - -
200A PHE* 3.8 26.2 - - + -
227A LEU* 4.1 21.3 - - + +
228A GLY* 4.3 8.5 - - - -
232A PHE* 4.3 11.4 - - + -
313A VAL* 6.1 2.0 - - + -
316A SER* 5.5 2.7 - - - +
340A VAL 2.9 9.2 + - - -
341A GLY* 3.5 7.5 - - - -
343A GLN* 3.2 49.1 + - + +
344A THR* 3.6 13.6 + - + +
349A VAL* 4.2 20.4 - - + -
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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