Contacts of the strand formed by residues 322 - 328 (chain A) in PDB entry 6N8P
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 322 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A VAL 3.4 2.1 - - - +
318A ILE* 3.3 5.9 - - - +
319A HIS 3.0 34.0 + - - +
320A ASP* 3.4 16.7 + - + +
321A GLY* 1.3 88.8 + - - +
323A GLN* 1.3 61.4 + - - +
324A THR* 5.9 0.4 - - - +
371A TRP* 3.9 16.9 - - + -
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Residues in contact with GLN 323 (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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274A PRO* 4.5 8.3 + - - +
275A TYR* 3.4 26.3 + - - -
300A PHE* 4.8 0.9 - - - -
316A SER* 4.6 3.1 - - - -
317A VAL 3.4 2.2 - - - -
318A ILE* 3.5 48.3 - - + +
321A GLY 4.2 2.3 + - - -
322A GLN* 1.3 72.9 - - - +
324A THR* 1.3 67.0 + - - +
371A TRP* 4.6 0.4 - - - -
487A TRP* 3.5 29.6 - - + -
489A PRO* 3.3 22.3 - - + +
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Residues in contact with THR 324 (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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315A ILE 3.7 0.7 - - - +
316A SER* 3.4 2.1 - - - -
317A VAL 3.2 29.3 + - - -
322A GLN* 5.9 0.5 - - - +
323A GLN* 1.3 77.3 + - - +
325A ALA* 1.3 61.2 + - - +
326A PHE* 3.3 38.9 + - + -
371A TRP* 3.6 24.3 - - - -
489A PRO* 3.7 6.7 - - - +
491A ARG* 3.8 30.5 + - + +
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Residues in contact with ALA 325 (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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275A TYR* 3.6 21.1 - - + +
304A MET* 4.6 6.7 - - - -
314A CYS* 4.7 2.2 - - + -
315A ILE 3.9 5.4 - - - -
316A SER* 3.8 8.1 - - - +
324A THR* 1.3 68.8 - - - +
326A PHE* 1.3 64.0 + - - +
327A ASP 3.1 0.9 + - - -
488A PRO* 4.8 0.4 - - + -
489A PRO* 2.6 24.8 + - + +
490A LEU* 3.3 23.7 - - + +
491A ARG 2.9 23.8 + - - -
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Residues in contact with PHE 326 (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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314A CYS* 3.3 3.7 - - - -
315A ILE* 2.9 47.1 + - + +
317A VAL* 3.9 18.8 - - + -
324A THR* 3.6 24.9 - - + -
325A ALA* 1.3 68.9 - - - +
327A ASP* 1.3 59.7 + - - +
328A PHE* 3.3 22.9 - - + -
353A LEU* 4.5 9.6 - - + -
364A ILE* 3.7 32.5 - - + -
366A LEU* 5.4 0.9 - - + -
371A TRP* 3.8 25.4 - + + -
491A ARG* 3.6 32.8 - - - -
493A VAL* 3.5 24.2 - - + -
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Residues in contact with ASP 327 (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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312A ARG* 2.9 40.7 + - - +
313A HIS 3.4 6.9 + - - +
314A CYS* 3.2 25.8 - - - -
325A ALA 3.1 4.6 + - - +
326A PHE* 1.3 73.6 - - - +
328A PHE* 1.3 64.7 + - - +
490A LEU* 4.3 7.0 - - + -
491A ARG 2.8 14.4 + - - +
492A LYS* 2.9 39.7 + - + +
493A VAL* 3.1 26.7 + - - +
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Residues in contact with PHE 328 (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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312A ARG* 5.8 0.2 - - - -
313A HIS* 3.1 31.1 + - - +
315A ILE* 3.9 23.8 - - + -
326A PHE* 3.3 29.2 - - + -
327A ASP* 1.3 83.2 - - - +
329A THR* 1.3 61.2 + - - +
330A SER 3.2 19.3 + - - +
332A VAL* 3.6 14.8 - - + -
353A LEU* 5.8 0.7 - - + -
355A VAL* 3.5 39.0 - - + -
357A ALA* 4.8 11.2 - - + -
360A GLU* 5.3 2.7 - - - +
362A VAL* 4.1 18.8 - - + -
364A ILE* 6.3 0.9 - - + -
492A LYS* 3.7 4.9 + - - -
493A VAL* 3.5 30.1 - - + +
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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