Contacts of the strand formed by residues 286 - 293 (chain B) in PDB entry 5NC5
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 286 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B VAL 3.3 10.8 - - - +
143B ILE* 3.8 12.3 - - + -
151B GLN* 3.5 22.1 + - - +
154B ILE* 4.1 2.5 - - - -
178B PHE 4.9 1.2 - - - +
279B ALA* 3.4 22.9 + - - +
281B PHE* 4.1 4.7 - - + +
284B GLN 3.4 4.7 + - - +
285B PRO* 1.3 75.5 - - - +
287B SER* 1.3 61.4 + - - +
610B PHE* 3.6 32.3 - - + -
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Residues in contact with SER 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLY* 3.5 4.9 - - - -
142B VAL* 2.9 28.1 + - - +
154B ILE* 4.1 10.7 - - - +
155B SER* 3.6 32.4 + - - -
158B VAL* 4.8 3.6 - - - -
177B LEU* 3.4 19.3 - - - +
178B PHE* 3.3 22.0 + - - -
279B ALA* 5.6 1.3 - - - -
286B ALA* 1.3 80.7 - - - +
288B GLY* 1.3 64.1 + - - +
610B PHE* 3.9 7.5 - - - -
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Residues in contact with GLY 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL 2.9 15.3 - - - -
141B GLY* 4.0 1.8 - - - -
142B VAL* 4.1 6.0 - - - +
158B VAL* 5.0 2.4 - - - +
177B LEU* 3.5 13.0 - - - +
178B PHE* 3.0 36.6 + - - +
287B SER* 1.3 81.8 + - - +
289B LEU* 1.3 64.1 + - - +
610B PHE* 5.5 0.7 - - - -
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Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B MET 4.1 0.2 - - - +
139B VAL* 3.3 5.4 - - - +
140B VAL* 2.7 43.4 + - + +
142B VAL* 5.8 0.4 - - + -
158B VAL* 3.8 21.1 - - + -
162B MET* 4.3 20.9 - - + -
163B LYS* 4.3 19.3 - - + -
166B ILE* 3.7 33.7 - - + -
175B VAL* 3.7 23.3 - - + -
176B GLN 3.3 4.9 - - - +
177B LEU* 4.5 1.6 - - - -
178B PHE* 4.3 4.6 - - - -
288B GLY* 1.3 81.1 - - - +
290B GLY* 1.3 61.1 + - - +
291B ILE* 3.8 10.1 + - + +
310B LEU* 5.5 0.4 - - + -
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Residues in contact with GLY 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B PHE* 3.7 25.2 - - - -
138B MET 4.1 1.8 - - - -
139B VAL* 4.5 0.4 - - - -
174B ASP 3.7 1.2 - - - +
175B VAL* 3.4 3.6 - - - -
176B GLN* 2.7 42.2 + - - +
178B PHE* 3.8 13.7 - - - -
289B LEU* 1.3 72.5 - - - +
291B ILE* 1.3 60.1 + - - -
292B LYS* 4.1 2.4 + - - +
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Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B PHE* 3.3 4.9 - - - -
137B LEU* 2.7 35.0 + - + +
138B MET* 3.0 20.8 + - + +
140B VAL* 4.1 26.5 - - + -
166B ILE* 3.6 26.9 - - + -
172B VAL* 3.9 22.4 - - + -
174B ASP 3.5 5.2 - - - +
175B VAL* 4.4 5.8 - - + -
289B LEU* 4.3 16.4 - - + +
290B GLY* 1.3 76.0 - - - +
292B LYS* 1.3 60.3 + - - +
306B ILE* 3.6 33.9 - - + -
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Residues in contact with LYS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LYS 5.6 1.0 + - - -
133B SER* 3.3 46.7 + - - +
134B SER 4.3 0.6 - - - +
135B SER* 4.2 14.8 - - - +
136B PHE* 4.2 31.6 - - + -
137B LEU* 4.0 6.0 - - - +
172B VAL* 3.7 5.9 - - - -
173B GLY 3.0 23.3 + - - -
174B ASP* 3.1 39.4 + - + +
176B GLN* 5.2 8.6 + - - -
290B GLY 4.6 3.4 - - - +
291B ILE* 1.3 82.7 - - - +
293B LEU* 1.3 63.6 + - - +
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B VAL 4.2 6.7 - - - +
33B ALA* 4.7 10.8 - - + -
135B SER 5.0 2.0 + - - -
137B LEU* 4.1 19.5 - - + +
171B GLY 3.6 8.3 - - - +
173B GLY* 4.0 2.2 - - - -
292B LYS* 1.3 77.3 - - - +
294B ALA* 1.3 73.4 + - - +
295B THR 3.8 0.3 + - - -
296B GLY 5.7 0.4 - - - +
297B ALA* 3.5 43.7 - - + +
299B ALA* 4.0 25.8 - - + +
302B THR* 3.6 22.7 - - + +
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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