Contacts of the strand formed by residues 386 - 391 (chain A) in PDB entry 3Q6N
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 ARG 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A TYR* 4.3 12.0 + - + -
316A LEU* 4.8 2.7 - - + -
317A THR* 3.8 41.6 + - + +
341A LEU* 3.5 0.5 - - - -
342A PHE* 2.6 45.2 + - + +
344A PRO* 4.0 17.8 - - + +
348A PRO* 4.0 25.9 - - - +
360A ASN* 4.5 20.2 - - - +
361A ILE* 3.9 2.9 - - - -
383A ASN 5.3 2.3 + - - -
384A PHE* 3.3 18.0 + - - +
385A ILE* 1.3 76.3 - - - +
387A GLY* 1.3 56.1 + - - +
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Residues in contact with GLY 387 (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 PHE* 5.8 0.2 - - - -
316A LEU* 4.0 17.3 - - - +
340A LEU 3.0 13.9 - - - -
341A LEU* 4.3 0.7 - - - -
342A PHE* 4.5 2.9 - - - -
360A ASN 4.2 3.6 + - - +
361A ILE* 3.4 16.9 - - - +
362A LYS* 3.0 24.1 + - - +
386A ARG* 1.3 75.3 - - - +
388A VAL* 1.3 66.1 + - - +
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Residues in contact with VAL 388 (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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299A ARG* 3.4 46.9 - - + +
312A PHE* 3.9 29.4 - - + -
316A LEU* 4.5 8.5 - - + -
339A ALA* 3.4 2.8 - - - +
340A LEU* 2.9 35.9 + - + +
341A LEU* 4.5 0.6 - - - +
361A ILE* 4.3 0.7 - - - -
362A LYS* 3.1 15.7 - - + +
364A TYR* 4.1 17.9 - - + +
387A GLY* 1.3 78.2 - - - +
389A VAL* 1.3 67.6 + - - +
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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
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337A PHE* 4.0 21.3 - - + -
338A ARG 3.4 2.7 - - - -
339A ALA* 4.1 5.2 - - + -
341A LEU* 4.9 1.8 - - + -
361A ILE* 4.1 12.3 - - + +
362A LYS 2.9 7.4 + - - +
363A LEU* 3.4 24.9 - - + +
364A TYR 2.9 26.3 + - - +
377A LEU* 4.7 2.5 - - + -
388A VAL* 1.3 79.2 - - - +
390A ASP* 1.3 65.2 + - - +
391A SER* 4.8 0.7 - - - +
412A ILE* 4.1 15.7 - - + -
416A LEU* 3.9 38.6 - - + -
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Residues in contact with ASP 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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299A ARG* 3.3 32.0 - - + +
300A ASN* 4.7 1.4 - - - +
337A PHE* 3.2 3.6 - - - +
338A ARG* 2.8 46.2 + - + +
364A TYR* 3.0 21.3 - - + +
366A ARG 3.3 2.1 + - - -
367A ARG* 2.7 57.6 + - - +
388A VAL* 4.1 1.2 - - - +
389A VAL* 1.3 73.7 - - - +
391A SER* 1.3 60.7 + - - +
392A GLU* 5.5 0.2 - - - +
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Residues in contact with SER 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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335A LEU* 4.1 8.8 - - - +
336A GLU 3.7 4.3 + - - -
337A PHE* 3.7 14.5 - - - +
363A LEU* 4.9 3.1 - - - -
364A TYR 2.9 12.2 + - - -
365A VAL* 3.6 5.7 - - - -
366A ARG* 2.8 28.2 + - - +
389A VAL* 4.9 3.8 - - - -
390A ASP* 1.3 75.3 + - - +
392A GLU* 1.3 73.1 + - - +
393A ASP 3.1 28.9 + - - -
412A ILE* 4.8 11.2 - - - -
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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