Contacts of the strand formed by residues 391 - 396 (chain A) in PDB entry 7NPA
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 PHE 391 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A ARG* 3.9 0.3 - - - -
356A ILE* 2.9 40.3 + - + +
364A TYR* 3.8 43.2 + + + -
369A ALA* 4.4 21.8 - - + -
372A ILE* 3.8 39.9 - - + -
373A LEU* 5.0 9.9 - - + -
383A ILE* 4.1 14.6 - - + -
384A LYS 3.8 3.1 - - - -
385A MET* 3.5 31.2 - - + -
390A ALA* 1.3 73.8 - - - +
392A GLU* 1.3 59.9 + - - +
393A ILE* 5.3 2.2 - - + -
369B ALA* 6.1 0.7 - - + -
383B ILE* 5.9 0.4 - - + -
385B MET* 4.6 9.9 - - - -
391B PHE* 4.7 11.9 - + - -
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Residues in contact with GLU 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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353A PHE* 3.6 26.7 - - + -
354A ILE 3.5 6.1 - - - +
355A ARG* 2.6 46.5 + - + -
382A LYS 3.5 1.2 - - - +
383A ILE* 3.8 1.6 - - - +
384A LYS* 2.8 57.4 + - + +
386A THR* 3.9 17.1 - - + +
391A PHE* 1.3 74.3 - - - +
393A ILE* 1.3 63.4 + - - +
394A HIS* 2.7 27.8 + - + +
429B PRO* 4.7 3.1 - - - +
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Residues in contact with ILE 393 (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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352A TYR 3.9 1.0 - - - +
353A PHE* 3.1 3.1 - - - -
354A ILE 2.9 39.7 + - - +
356A ILE* 4.3 13.5 - - + -
372A ILE* 4.2 21.3 - - + +
375A ILE* 5.1 0.2 - - + -
376A ALA* 3.9 23.6 - - + +
381A GLY* 3.7 25.4 - - - -
382A LYS 3.4 5.8 - - - +
383A ILE* 4.3 12.1 - - + -
391A PHE 5.1 0.9 - - - -
392A GLU* 1.3 78.1 - - - +
394A HIS* 1.3 62.6 + - - +
396A ILE* 4.0 6.0 - - + +
404A MET* 3.3 35.7 - - + -
408A LEU* 4.7 5.8 - - + -
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Residues in contact with HIS 394 (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 ARG* 2.9 36.7 + - + +
352A TYR 3.9 2.5 - - - -
353A PHE* 3.7 23.5 - + + +
380A ASP 4.2 0.2 - - - +
381A GLY* 3.2 8.6 - - - -
382A LYS* 2.8 44.3 + - + +
384A LYS* 3.9 25.2 - - + +
392A GLU* 2.7 31.9 + - + -
393A ILE* 1.3 76.3 - - - +
395A GLY* 1.3 60.3 + - - +
396A ILE 3.6 1.3 - - - -
363B TRP* 3.9 19.4 - + + -
429B PRO* 4.6 12.1 - - + +
433B ASN* 4.7 4.5 - - + -
434B CYS* 6.0 0.7 - - - -
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Residues in contact with GLY 395 (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 ARG* 3.4 9.5 - - - +
351A THR* 3.5 24.9 - - - +
352A TYR 3.0 7.0 + - - -
379A TYR 4.8 2.1 - - - +
380A ASP* 4.3 11.6 - - - +
382A LYS* 5.8 1.1 - - - -
394A HIS* 1.3 75.8 - - - +
396A ILE* 1.3 64.7 + - - +
397A SER 3.6 1.9 + - - -
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Residues in contact with ILE 396 (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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351A THR* 3.4 3.1 - - - -
352A TYR* 2.7 44.5 + - - +
354A ILE* 4.1 7.4 - - + -
376A ALA 5.2 0.2 - - - +
379A TYR* 3.7 21.8 - - + +
381A GLY* 3.8 22.9 - - - -
393A ILE* 4.0 13.0 - - + +
394A HIS 4.3 0.2 - - - +
395A GLY* 1.3 75.3 - - - +
397A SER* 1.3 77.1 + - - +
400A ASP* 3.9 16.4 - - + -
401A VAL* 3.9 18.4 - - + +
404A MET* 3.6 37.7 - - + -
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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