Contacts of the strand formed by residues 392 - 397 (chain A) in PDB entry 3Q7I
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 VAL 392 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ASN* 5.6 0.7 + - - +
325A ALA* 3.4 15.7 - - + -
327A LEU* 3.5 23.1 - - + -
383A LEU* 4.3 17.5 - - + -
390A ILE 3.5 11.6 + - - +
391A PRO* 1.3 78.9 - - - +
393A ASP* 1.3 66.8 + - - +
394A PHE* 3.4 33.2 - - + -
422A LEU* 4.3 12.3 - - + -
459A PRO 3.8 15.9 + - - +
460A SER* 3.1 5.1 - - - +
461A THR* 2.9 24.6 + - - -
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Residues in contact with ASP 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A MET* 4.7 4.4 - - - +
324A GLN* 6.0 0.9 - - - -
325A ALA 2.9 10.0 + - - +
326A LEU* 3.5 12.4 - - + +
327A LEU* 2.8 34.8 + - - +
392A VAL* 1.3 77.7 - - - +
394A PHE* 1.3 57.1 + - - +
395A ILE* 4.9 0.4 - - + -
461A THR* 3.4 29.2 + - + +
463A ILE* 5.1 2.0 - - + -
480A TYR* 2.7 37.6 + - - +
483A LYS* 4.5 9.4 + - - -
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Residues in contact with PHE 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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327A LEU* 3.5 27.6 - - + -
329A TYR* 3.6 27.1 - + - -
380A HIS* 4.6 1.6 - + - -
392A VAL* 3.4 19.7 - - + -
393A ASP* 1.3 72.8 - - - +
395A ILE* 1.3 64.9 + - - +
415A CYS* 3.8 23.6 - - - -
418A GLN* 3.8 19.1 - - + -
419A SER* 3.6 39.7 - - - -
422A LEU* 3.9 10.5 - - + -
460A SER* 3.8 8.3 - - - -
461A THR 2.8 18.1 + - - +
462A THR* 3.5 11.2 - - + +
463A ILE* 2.9 27.4 + - - +
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Residues in contact with ILE 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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326A LEU* 3.9 18.4 - - + -
327A LEU 3.0 5.5 + - - -
328A PRO* 4.0 14.4 - - + -
329A TYR* 2.8 34.5 + - - +
333A LEU* 4.2 13.4 - - + +
336A PHE* 4.5 10.1 - - + -
393A ASP* 4.9 0.7 - - + -
394A PHE* 1.3 80.2 - - - +
396A ALA* 1.3 61.8 + - - +
397A ILE* 4.2 11.9 - - + +
415A CYS* 5.0 0.2 - - - -
463A ILE* 3.4 23.1 - - + +
465A LEU* 4.6 5.6 - - + -
476A LEU* 4.1 29.2 - - + -
480A TYR* 3.6 25.1 - - + +
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Residues in contact with ALA 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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329A TYR* 4.7 4.9 - - - -
394A PHE 4.1 0.6 - - - -
395A ILE* 1.3 74.1 - - - +
397A ILE* 1.3 67.0 + - - +
412A LEU* 4.0 13.5 - - + -
415A CYS* 4.0 22.0 - - + -
416A PHE* 4.2 7.9 - - + -
462A THR* 4.5 4.9 - - + -
463A ILE 2.9 9.9 + - - +
464A LEU* 3.3 19.8 - - + -
465A LEU* 2.9 25.5 + - - +
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Residues in contact with ILE 397 (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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329A TYR 4.8 4.1 + - - +
330A ASP* 3.9 32.8 - - + +
332A ARG* 4.1 8.5 - - - +
333A LEU* 4.4 4.5 - - + -
395A ILE* 4.2 13.7 - - + +
396A ALA* 1.3 83.6 - - - +
398A ALA* 1.3 55.0 + - - +
399A THR 3.3 23.1 - - - +
400A SER* 5.2 0.2 - - - -
408A GLN* 2.7 30.8 + - - +
411A LEU* 5.6 1.5 - - + +
412A LEU* 3.5 9.6 - - - +
465A LEU* 3.6 28.3 - - + -
467A GLU 3.6 4.3 - - - -
468A LEU* 3.5 34.1 - - + +
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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