Contacts of the strand formed by residues 382 - 387 (chain A) in PDB entry 2XFN
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 HIS 382 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ASN* 4.3 2.6 + - - -
50A LYS* 3.7 38.0 - - + +
51A VAL* 3.5 26.7 - - + +
299A VAL* 3.8 1.4 - - - -
300A TYR* 2.9 42.9 + + + +
357A LYS* 5.7 1.1 - - - -
361A LEU* 5.6 1.6 - - - -
380A PRO* 3.6 7.4 - - - +
381A VAL* 1.3 84.5 + - + +
383A TYR* 1.3 78.0 + - - +
384A GLU* 2.7 29.2 + - + -
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Residues in contact with TYR 383 (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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297A CYS* 3.3 29.6 - - + +
298A ILE 3.2 16.6 - - - -
299A VAL* 3.8 13.0 - - + -
357A LYS* 3.1 62.1 + - + -
360A ARG* 4.0 8.5 - - - +
361A LEU* 3.7 45.3 - - + -
364A LEU* 4.0 5.2 - - + +
382A HIS* 1.3 84.9 + - - +
384A GLU* 1.3 78.0 + - - +
385A GLU* 2.7 37.9 + - + -
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Residues in contact with GLU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.4 21.8 - - + +
48A ASN* 3.0 18.4 + - - -
51A VAL* 3.9 13.0 - - + -
54A VAL* 4.5 4.0 - - + -
56A LEU* 4.2 18.0 - - + +
297A CYS* 3.6 0.2 - - - -
298A ILE* 2.7 38.2 + - + +
300A TYR* 4.2 7.6 - - + -
357A LYS* 3.9 12.1 + - - +
382A HIS* 2.7 33.5 + - + +
383A TYR* 1.3 78.6 - - - +
385A GLU* 1.3 66.2 + - - +
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Residues in contact with GLU 385 (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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56A LEU* 4.2 12.3 - - - +
295A ILE* 4.3 8.0 - - + +
296A LYS 3.2 12.8 - - - +
297A CYS* 4.1 4.3 - - - -
357A LYS* 3.6 19.8 - - + +
360A ARG* 2.8 45.1 + - - -
383A TYR* 2.7 43.2 + - + +
384A GLU* 1.3 80.8 + - - +
386A LYS* 1.3 66.8 - - - +
387A ASN* 5.6 0.9 - - - +
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Residues in contact with LYS 386 (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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44A TYR* 5.6 4.5 - - + -
56A LEU* 4.0 23.8 - - + +
295A ILE* 3.3 5.5 - - - -
296A LYS 2.9 31.3 + - - +
385A GLU* 1.3 79.1 - - - +
387A ASN* 1.3 76.5 + - - +
388A TRP* 3.5 39.7 - - + +
390A GLU* 2.7 23.5 + - - +
391A GLU* 2.6 39.4 + - - -
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Residues in contact with ASN 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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294A VAL 3.7 6.2 - - - +
295A ILE* 3.7 26.2 - - + +
349A ALA 4.3 1.0 + - - -
353A ALA* 3.6 15.6 - - - +
360A ARG* 6.3 0.4 - - - -
385A GLU* 5.6 1.0 - - - +
386A LYS* 1.3 77.5 - - - +
388A TRP* 1.3 58.7 + - - +
389A CYS* 3.0 27.5 + - - +
390A GLU* 3.2 38.5 + - - +
280B MET* 2.8 35.6 - - - +
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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