Contacts of the strand formed by residues 172 - 177 (chain A) in PDB entry 3NBN
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 LYS 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A LEU* 6.0 1.3 - - + -
40A LYS* 5.8 1.1 - - - +
145A LYS* 5.8 1.6 - - - +
170A GLY 3.6 2.6 + - - -
171A THR* 1.3 75.4 + - - +
173A VAL* 1.3 63.2 + - - +
205A ALA* 4.4 11.2 - - + +
206A PHE 3.1 14.1 - - - +
207A PHE* 3.7 31.8 - - + -
239A SER* 5.8 0.2 - - - +
319A THR* 2.9 43.6 + - + +
320A ASP* 3.9 33.9 + - - +
321A LYS* 4.0 30.4 - - - +
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Residues in contact with VAL 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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167A ILE* 4.1 9.4 - - + -
171A THR* 3.5 17.9 - - - +
172A LYS* 1.3 79.9 - - - +
174A ALA* 1.3 60.9 + - - +
175A LEU* 5.0 6.0 - - + +
205A ALA* 4.5 1.6 - - - -
206A PHE* 2.5 48.1 + - + +
208A ILE* 4.0 29.2 - - + -
236A LEU* 5.8 0.9 - - + -
316A ILE* 3.6 26.2 - - + -
317A ILE 3.3 10.8 - - - +
318A SER* 3.5 16.2 - - - +
319A THR* 4.0 2.5 - - - +
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Residues in contact with ALA 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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55A PRO* 5.0 6.7 - - + -
173A VAL* 1.3 75.9 - - - +
175A LEU* 1.3 61.1 + - - +
176A PHE* 5.9 0.4 - - - -
203A TRP* 3.7 31.0 - - + -
204A GLY 3.6 21.1 - - - +
205A ALA* 4.7 0.7 - - - -
206A PHE* 4.9 0.7 - - - -
317A ILE* 2.9 40.7 + - + +
319A THR* 4.5 6.1 - - - +
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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 VAL* 5.0 5.8 - - + +
174A ALA* 1.3 77.6 - - - +
176A PHE* 1.3 59.5 + - - +
188A TYR* 3.9 3.8 - - - +
189A LEU* 3.3 58.0 + - + +
204A GLY 5.1 0.6 + - - -
206A PHE* 4.5 9.8 - - + -
208A ILE* 5.7 0.9 - - + -
236A LEU* 4.6 10.3 - - + -
274A PHE* 3.5 37.2 - - + -
284A LEU* 6.4 0.9 - - + -
314A TRP* 3.8 18.1 - - + -
315A THR 3.2 16.2 - - - +
316A ILE* 3.6 21.8 - - + -
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Residues in contact with PHE 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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54A CYS* 3.5 45.1 - - + -
55A PRO* 4.3 11.2 - - + -
174A ALA 5.4 0.4 - - - -
175A LEU* 1.3 73.0 - - - +
177A ASN* 1.3 59.3 + - - +
178A ARG* 3.5 39.5 - - + -
186A THR* 4.5 0.9 - - + -
187A ARG 3.8 4.3 - - - +
188A TYR* 3.0 29.4 - - + -
269A LEU* 4.1 13.5 - - + -
314A TRP* 3.5 5.9 - - - -
315A THR* 2.8 76.2 + - + -
317A ILE* 4.6 5.4 - - + -
7X G 4.9 3.4 - - - -
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Residues in contact with ASN 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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176A PHE* 1.3 73.8 - - - +
178A ARG* 1.3 68.6 + - - +
179A LEU* 3.2 27.5 - - - +
186A THR* 3.5 0.7 + - - -
187A ARG* 2.7 44.8 + - - +
286A LEU* 3.2 25.6 - - + +
310A ASP 3.4 16.2 + - - -
311A GLY 4.2 3.8 + - - -
313A SER 2.8 30.4 + - - -
314A TRP* 3.7 18.6 - - + -
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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