Contacts of the strand formed by residues 369 - 375 (chain B) in PDB entry 3NUI
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 ILE 369 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B ILE* 3.7 22.2 - - + +
364B ALA* 3.7 26.9 - - + +
366B ARG* 3.2 14.7 + - + +
368B ASN* 1.3 85.9 - - - +
370B GLY* 1.3 64.5 + - - +
371B GLU 3.4 28.0 - - - +
381B LEU* 4.0 22.7 - - + -
382B GLU 3.4 9.9 - - - +
383B ALA* 4.7 1.6 - - + -
384B VAL* 3.8 1.8 - - - -
387B LYS* 3.1 24.4 + - - -
403B ILE* 5.8 0.2 - - + -
445B LEU* 4.3 13.9 - - + -
449B PHE* 3.8 20.4 - - + -
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Residues in contact with GLY 370 (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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185B TRP* 3.5 30.9 + - - -
364B ALA 5.7 0.2 - - - -
369B ILE* 1.3 75.8 - - - +
371B GLU* 1.3 60.7 + - - +
382B GLU 2.7 15.5 + - - -
384B VAL* 3.4 22.0 - - - +
387B LYS* 4.4 13.1 - - - +
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Residues in contact with GLU 371 (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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183B HIS* 2.5 31.8 + - - -
185B TRP* 3.2 40.1 - - + +
364B ALA* 4.6 3.8 - - - -
369B ILE* 3.4 14.7 - - - +
370B GLY* 1.3 77.6 - - - +
372B TYR* 1.3 72.8 + - - +
373B ARG* 2.8 30.3 + - - +
380B ALA 4.0 0.3 - - - +
381B LEU* 3.7 0.7 - - - -
382B GLU* 3.0 29.9 + - + +
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Residues in contact with TYR 372 (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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357B GLU* 2.5 46.1 + - + +
360B LEU* 3.9 22.7 - - + +
361B LYS* 3.7 42.2 - - + +
364B ALA* 4.1 11.4 - - + +
371B GLU* 1.3 85.4 - - - +
373B ARG* 1.3 68.9 + - - +
379B TRP* 3.8 16.2 - + - -
380B ALA 3.3 6.7 - - - +
381B LEU* 3.7 20.0 - - + -
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Residues in contact with ARG 373 (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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183B HIS* 3.4 17.9 - - + -
229B GLY 5.4 0.2 + - - -
230B GLY* 3.1 32.1 + - - -
231B VAL* 3.1 14.4 + - - +
232B ILE* 3.9 12.4 - - - +
233B PRO* 3.9 10.1 - - + -
371B GLU* 2.8 38.2 + - - +
372B TYR* 1.3 79.9 - - - +
374B GLY* 1.3 56.6 + - - +
379B TRP* 3.2 10.6 - - - -
380B ALA* 2.7 42.6 + - + +
382B GLU* 2.8 32.0 + - - +
420B SER* 2.6 30.5 + - - -
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Residues in contact with GLY 374 (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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231B VAL* 4.2 4.5 - - - -
233B PRO* 3.5 20.7 - - - +
373B ARG* 1.3 76.9 - - - +
375B ILE* 1.3 67.4 + - - +
378B MET 3.0 15.3 - - - -
379B TRP* 3.4 18.0 - - - -
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Residues in contact with ILE 375 (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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225B VAL* 3.4 28.3 - - + -
233B PRO* 4.3 2.7 - - + -
264B ARG 3.7 0.7 - - - +
265B THR* 3.9 23.6 - - + +
273B THR* 5.0 5.4 - - - +
274B TYR* 3.5 24.7 - - + +
374B GLY* 1.3 77.5 - - - +
376B GLY* 1.3 71.4 + - - +
377B PHE 3.1 0.3 + - - -
378B MET* 3.0 38.5 + - + +
379B TRP* 3.6 11.7 - - - -
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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