Contacts of the strand formed by residues 388 - 392 (chain A) in PDB entry 3NIG
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 GLN 388 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A ALA* 4.6 0.2 - - - +
378A ALA* 2.8 35.8 + - + +
381A GLY 4.1 0.6 + - - -
382A GLY* 3.6 30.5 + - - +
383A PRO* 4.2 6.5 - - - +
387A GLY* 1.3 73.6 - - - +
389A VAL* 1.3 66.2 + - - +
390A LEU* 3.9 20.8 - - + +
406A VAL* 3.1 28.8 - - + +
407A LEU 3.3 6.3 - - - +
408A ASP* 2.7 33.2 + - - +
417A PHE* 4.0 2.7 - - - +
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Residues in contact with VAL 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ALA* 3.8 28.3 - - + -
376A VAL 3.5 8.1 - - - +
377A ALA* 4.4 3.1 - - - -
388A GLN* 1.3 78.0 - - - +
390A LEU* 1.3 66.2 + - - +
391A VAL* 5.3 1.6 - - + -
405A GLN 4.2 0.2 - - - +
406A VAL* 3.5 2.4 - - - +
407A LEU* 2.8 49.1 + - + +
417A PHE* 3.7 19.7 - - + -
418A GLY* 4.1 11.9 - - - -
421A LEU* 3.9 23.1 - - + -
435A LEU* 4.3 14.1 - - + -
437A VAL* 4.2 3.1 - - + -
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Residues in contact with LEU 390 (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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356A PHE* 4.2 25.4 - - + -
375A ALA* 3.3 2.4 - - - -
376A VAL 2.8 42.8 + - - +
378A ALA* 4.6 5.2 - - + -
388A GLN* 3.9 32.3 - - + +
389A VAL* 1.3 81.6 - - - +
391A VAL* 1.3 63.1 + - - +
392A PHE* 3.7 22.8 - - + -
403A PRO* 4.1 24.2 - - + -
405A GLN 3.7 3.6 - - - -
406A VAL* 4.1 12.8 - - + -
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Residues in contact with VAL 391 (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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1A LEU 3.7 10.5 - - - +
3A LEU* 4.1 25.8 - - + -
363A LEU* 3.8 24.9 - - + -
366A LEU* 3.9 6.3 - - + -
374A ILE 3.4 3.4 - - - +
375A ALA* 4.7 5.8 - - + -
389A VAL* 5.3 0.2 - - + -
390A LEU* 1.3 73.9 - - - +
392A PHE* 1.3 60.3 + - - +
393A LEU* 3.9 10.1 - - + -
403A PRO* 3.0 6.2 - - - +
404A SER* 2.8 48.3 + - - +
405A GLN* 2.9 26.3 + - + +
407A LEU* 5.1 8.3 - - + -
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Residues in contact with PHE 392 (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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347A LEU* 3.8 26.5 - - + -
356A PHE* 3.9 31.4 - + - -
373A ASP* 3.4 3.1 - - - +
374A ILE* 2.9 44.1 + - + -
376A VAL* 4.1 15.9 - - + -
390A LEU* 3.7 29.8 - - + -
391A VAL* 1.3 75.9 - - - +
393A LEU* 1.3 64.2 + - - +
399A LEU* 3.7 10.9 - - + +
400A ARG 3.6 23.3 - - - +
401A SER 3.9 4.7 - - - -
402A ARG 4.0 1.6 - - - -
403A PRO* 3.7 37.9 - - + -
404A SER 4.8 0.2 - - - +
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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