Contacts of the strand formed by residues 361 - 365 (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 LEU 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A PHE* 3.8 15.9 - - + -
47A LEU* 3.8 14.1 - - + -
49A ILE* 5.3 0.2 - - + -
354A VAL* 3.7 22.2 - - + -
355A VAL 3.3 24.5 - - - +
356A LEU* 3.7 16.8 - - + -
360A GLU* 1.3 76.3 - - - +
362A VAL* 1.3 67.2 + - - +
363A VAL* 4.7 5.6 - - + -
376A LEU* 3.3 39.2 - - + +
378A TYR* 5.7 0.4 - - + -
379A LEU* 3.6 36.0 + - + +
381A SER* 4.4 0.6 + - - -
420A TRP* 5.0 7.4 - - + -
422A ILE* 5.8 0.2 - - + -
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Residues in contact with VAL 362 (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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328A PHE* 4.1 25.6 - - + -
353A LEU 3.4 1.8 - - - +
354A VAL* 3.5 2.6 - - - +
355A VAL* 2.8 42.3 + - + +
357A ALA* 5.5 0.9 - - + -
360A GLU* 4.3 12.1 - - + -
361A LEU* 1.3 78.3 - - - +
363A VAL* 1.3 67.4 + - - +
364A ILE* 3.9 27.4 - - + -
373A PRO* 5.7 3.1 - - + -
376A LEU* 5.3 0.4 - - - -
493A VAL* 4.1 17.3 - - + -
494A GLY* 4.0 26.5 - - - +
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Residues in contact with VAL 363 (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 ALA* 4.5 14.6 - - + -
353A LEU 3.3 6.1 - - - +
354A VAL* 4.1 26.7 - - + -
361A LEU* 4.4 4.7 + - + -
362A VAL* 1.3 79.7 - - - +
364A ILE* 1.3 61.2 + - - +
373A PRO* 3.5 5.4 - - - +
374A VAL* 2.8 63.4 + - + +
376A LEU* 4.1 10.6 - - + +
420A TRP* 3.8 28.5 - - + -
421A PRO* 4.9 6.3 - - + -
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Residues in contact with ILE 364 (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 PHE* 3.7 38.8 - - + -
328A PHE* 6.3 0.9 - - + -
352A ALA* 3.3 4.3 - - - +
353A LEU* 3.0 47.6 + - + +
355A VAL* 6.1 0.9 - - + -
362A VAL* 3.9 21.8 - - + -
363A VAL* 1.3 80.6 - - - +
365A ASP* 1.3 65.5 + - - +
366A LEU* 3.3 10.6 + - + +
371A TRP* 3.7 26.9 - - + +
372A PRO 3.8 1.1 - - - -
373A PRO* 4.0 19.3 - - + -
374A VAL* 4.3 2.5 - - - -
491A ARG* 4.7 0.2 - - - +
493A VAL* 4.2 11.2 - - + -
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Residues in contact with ASP 365 (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 TYR 3.8 3.6 - - - -
352A ALA* 4.9 0.2 - - - +
364A ILE* 1.3 70.0 - - - +
366A LEU* 1.3 60.2 + - - +
367A GLN* 3.0 15.4 + - - +
368A THR* 2.6 28.1 + - - +
371A TRP* 3.2 25.1 - - - -
372A PRO* 2.9 24.9 + - + +
374A VAL* 3.8 8.9 - - + +
416A SER* 2.5 31.8 + - - +
418A MET* 3.2 28.3 - - - +
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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