Contacts of the strand formed by residues 378 - 383 (chain A) 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 MET 378 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A TRP* 6.0 0.2 - - + -
225A VAL* 3.7 36.1 - - + +
226A MET 4.3 7.2 - - - +
227A GLY* 4.4 4.9 - - - -
231A VAL* 3.4 18.5 - - + +
259A ILE* 3.9 22.4 - - + -
260A CYS* 4.1 7.4 - - - -
264A ARG* 3.9 25.1 - - + +
265A THR* 3.9 23.8 - - - -
374A GLY* 3.1 4.2 - - - -
375A ILE* 3.0 36.9 + - + +
377A PHE* 1.3 80.7 - - - +
379A TRP* 1.4 62.3 + - - +
423A LEU 3.6 3.8 - - - -
424A CYS* 4.5 6.5 - - + +
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Residues in contact with TRP 379 (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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231A VAL* 3.7 5.7 - - - +
353A ALA* 4.4 7.2 - - + -
356A PHE* 3.4 33.9 - + + -
357A GLU* 3.8 35.2 - - + -
360A LEU* 3.4 31.4 - - + -
372A TYR* 3.8 25.4 - + - -
373A ARG 3.2 22.2 - - - +
374A GLY* 3.3 23.3 - - - -
375A ILE* 3.5 20.4 - - - -
376A GLY 2.8 26.2 + - - -
378A MET* 1.4 82.8 - - - +
380A ALA* 1.3 62.3 + - - +
422A VAL* 3.4 8.0 - - - +
423A LEU* 2.9 34.6 + - + +
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Residues in contact with ALA 380 (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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230A GLY 3.5 24.9 - - - +
231A VAL* 4.0 5.6 - - + +
360A LEU* 5.2 0.8 - - - +
372A TYR* 3.3 7.1 - - - +
373A ARG* 2.8 46.5 + - + +
379A TRP* 1.3 77.4 - - - +
381A LEU* 1.3 63.2 + - - +
420A SER* 4.4 3.4 - - - -
421A VAL 3.2 13.2 - - - +
422A VAL* 4.3 6.5 - - + -
423A LEU* 4.7 2.0 - - - +
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Residues in contact with LEU 381 (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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360A LEU* 3.7 30.3 - - + +
363A ILE* 4.0 26.9 - - + -
369A ILE* 4.2 17.3 - - + -
371A GLU 3.6 2.2 - - - +
372A TYR* 3.5 28.0 - - + -
380A ALA* 1.3 73.2 - - - +
382A GLU* 1.3 60.8 + - - +
383A ALA 4.0 0.9 + - - -
420A SER* 3.2 4.8 - - - -
421A VAL* 3.0 39.4 + - + +
423A LEU* 4.5 6.5 - - + -
441A LEU* 3.5 33.0 - - + -
445A LEU* 4.7 6.1 - - + -
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Residues in contact with GLU 382 (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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183A HIS* 4.6 1.2 - - - -
185A TRP* 3.9 21.7 - - + -
186A ARG* 2.6 32.5 + - - -
369A ILE* 3.4 7.4 - - - +
370A GLY* 2.7 31.7 + - - -
371A GLU* 3.1 20.0 + - + +
373A ARG* 2.4 44.6 + - - +
381A LEU* 1.3 71.6 - - - +
383A ALA* 1.3 65.0 + - - +
384A VAL* 4.7 0.4 - - + -
419A GLN* 3.7 19.2 + - - +
420A SER* 3.1 16.6 + - - +
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Residues in contact with ALA 383 (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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368A ASN 3.3 8.7 - - - +
369A ILE* 4.7 0.9 - - - +
381A LEU 4.0 1.4 + - - -
382A GLU* 1.3 77.7 - - - +
384A VAL* 1.3 66.3 - - - +
392A PRO* 4.6 4.9 - - - +
393A PHE* 4.6 6.0 + - + -
399A VAL* 4.2 27.8 - - + -
400A SER* 5.5 0.9 - - - +
403A ILE* 4.6 8.1 - - + -
419A GLN* 2.9 31.6 + - + +
449A PHE* 4.2 13.0 - - + -
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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