Contacts of the strand formed by residues 283 - 290 (chain B) in PDB entry 1NBI
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 TYR 283 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B ASN* 3.9 21.3 - - + -
173B ASP* 4.9 2.0 - - + -
174B HIS 3.5 6.3 - - - +
175B LYS* 3.5 41.4 + - + -
191B ASN* 2.9 33.8 + - - -
192B ILE* 4.2 14.1 - - + -
193B TYR* 3.6 43.7 - + + -
194B TYR* 3.3 19.6 - + - -
268B GLY 2.4 27.6 - - - +
269B ASP* 2.9 10.1 + - - +
281B PRO* 3.5 7.4 - - - +
282B CYS* 1.3 90.0 - - + +
284B PHE* 1.3 59.6 + - - +
285B ILE* 4.3 9.2 - - + -
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Residues in contact with PHE 284 (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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173B ASP* 3.1 23.1 - - - +
174B HIS* 2.9 40.8 + + + -
176B ASN* 3.8 34.5 - - - -
178B ASP* 4.7 4.5 - - + -
247B LEU* 3.2 38.4 - - + -
266B VAL* 3.8 2.7 - - + -
267B LEU 3.1 15.5 - - - -
273B TYR* 3.7 28.9 - + - -
281B PRO* 3.4 26.7 - - + -
283B TYR* 1.3 76.2 - - - +
285B ILE* 1.3 63.1 + - - +
286B HIS* 3.3 13.0 + - + -
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Residues in contact with ILE 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B TRP* 4.0 9.6 - - + -
136B LEU* 4.7 2.0 - - + -
171B VAL* 3.9 25.4 - - + -
172B ILE 4.7 1.6 - - - +
173B ASP* 3.7 15.0 - - + +
193B TYR* 3.3 24.2 - - - +
265B SER 3.6 1.7 - - - +
266B VAL* 3.5 1.4 - - - -
267B LEU* 2.9 42.1 + - + +
268B GLY 4.0 2.9 - - - +
269B ASP* 5.4 0.7 - - - -
270B PHE* 3.4 52.9 - - + +
283B TYR* 4.3 12.3 - - + -
284B PHE* 1.3 71.7 - - - +
286B HIS* 1.3 60.9 + - - +
287B VAL* 3.6 2.3 + - + -
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Residues in contact with HIS 286 (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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170B LEU 3.2 4.7 - - - +
171B VAL* 3.5 1.6 - - - -
172B ILE* 2.8 50.2 + - + +
174B HIS* 3.4 11.1 + + - -
247B LEU* 3.2 34.4 - - + +
250B PHE* 3.5 23.5 - + - -
251B THR* 3.6 24.0 - - - -
254B VAL* 4.1 2.0 - - + +
264B HIS* 3.3 17.4 + + - +
265B SER 3.5 4.3 - - - -
266B VAL* 3.3 18.6 - - + +
284B PHE* 3.5 13.8 - - - +
285B ILE* 1.3 72.2 - - - +
287B VAL* 1.3 60.2 + - - +
288B LEU* 3.9 8.9 - - + +
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Residues in contact with VAL 287 (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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47B TRP* 3.6 37.5 - - + -
51B LEU* 4.0 22.9 - - + -
169B LEU* 4.3 15.3 - - + -
170B LEU 3.2 5.2 - - - +
171B VAL* 4.5 5.2 - - + -
263B GLN 3.7 1.6 - - - +
264B HIS 3.8 0.2 - - - -
265B SER* 2.7 46.7 + - - +
267B LEU* 4.2 11.9 - - + -
285B ILE* 4.5 3.1 - - + +
286B HIS* 1.3 74.5 - - - +
288B LEU* 1.3 70.8 + - - +
289B LYS* 6.1 0.4 - - + -
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Residues in contact with LEU 288 (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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169B LEU* 3.0 11.9 - - - +
170B LEU* 2.7 52.9 + - + +
172B ILE* 5.1 0.2 - - + -
254B VAL* 4.4 12.1 - - + -
255B GLN* 4.5 1.6 - - + -
258B PHE* 3.7 23.1 - - + -
262B CYS* 3.9 25.8 - - - -
263B GLN 3.2 14.4 - - - +
264B HIS* 3.7 34.8 - - + +
286B HIS* 3.9 18.8 - - + +
287B VAL* 1.3 99.9 - - - +
289B LYS* 1.3 58.5 + - - +
290B LYS 4.0 0.8 + - - -
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Residues in contact with LYS 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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55B HIS* 3.6 28.0 + - + +
165B ARG* 5.0 3.6 - - - +
167B GLY* 3.3 39.5 + - - +
168B GLY 3.5 2.9 - - - +
169B LEU* 3.6 12.6 - - + -
262B CYS* 3.2 3.2 - - - -
263B GLN* 2.8 63.6 + - + +
288B LEU* 1.3 73.6 - - - +
290B LYS* 1.3 62.5 + - - +
291B THR* 3.4 5.7 + - + +
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Residues in contact with LYS 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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161B ALA* 3.2 22.8 + - - +
162B SER* 4.0 12.3 + - - +
164B VAL* 3.3 28.6 + - + +
165B ARG 4.2 0.7 - - - +
166B PRO* 3.9 19.3 - - + -
167B GLY* 2.5 35.2 + - - -
168B GLY 3.2 11.5 + - - +
258B PHE* 3.7 27.4 - - + +
261B ARG 4.0 4.5 - - - +
262B CYS* 4.2 4.2 - - - +
288B LEU 4.0 1.8 + - - -
289B LYS* 1.3 72.5 - - - +
291B THR* 1.3 59.7 + - - +
292B GLY* 3.5 33.0 - - - +
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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