Contacts of the strand formed by residues 397 - 406 (chain B) in PDB entry 2XAR
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 397 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275B PHE 3.2 15.9 - - - +
276B ILE* 3.6 4.4 - - - +
277B GLN* 3.1 58.0 + - - +
377B SER* 4.0 9.1 + - - +
391B SER* 3.7 2.9 - - - -
392B LEU* 3.0 30.4 + - - +
395B THR* 3.2 29.3 + - - +
396B ASN* 1.3 77.7 - - - +
398B THR* 1.3 65.0 + - - +
399B PHE* 3.5 27.7 - - + -
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Residues in contact with THR 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B SER* 3.7 2.1 + - - -
378B ARG* 2.9 63.7 + - - +
389B TYR* 3.4 35.7 - - + -
390B VAL 3.6 6.3 - - - +
391B SER* 4.7 5.9 + - - +
396B ASN 5.5 0.2 - - - -
397B GLN* 1.3 76.4 + - - +
399B PHE* 1.3 69.1 + - - +
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Residues in contact with PHE 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B PHE* 3.4 45.1 - + - -
276B ILE* 4.4 9.6 - - + -
290B LEU* 3.6 31.0 - - + -
375B PHE* 4.4 7.1 - - + -
376B GLN 3.2 9.6 - - - +
377B SER* 3.6 26.7 - - - -
389B TYR* 3.0 5.5 - - - -
390B VAL* 2.9 39.8 + - - +
392B LEU* 3.9 20.6 - - + -
397B GLN* 3.5 39.7 - - + -
398B THR* 1.3 73.8 - - - +
400B ASP* 1.3 66.2 + - - +
401B TYR* 3.7 2.1 + - - +
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Residues in contact with ASP 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B PHE* 3.4 23.1 - - + -
375B PHE* 3.6 1.7 - - - -
376B GLN* 2.9 36.6 + - + +
378B ARG* 2.9 33.1 + - - +
384B GLU 3.2 14.0 + - - +
385B PRO* 3.0 24.5 - - - +
386B SER* 2.8 26.9 + - - +
388B ASP 3.3 5.9 - - - +
389B TYR* 3.4 1.2 - - - +
398B THR 4.3 0.6 - - - -
399B PHE* 1.3 73.1 - - - +
401B TYR* 1.3 58.8 + - - +
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Residues in contact with TYR 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B PHE* 3.8 3.5 - - - -
294B ALA* 4.1 14.8 - - + -
297B GLY* 4.0 4.0 - - - -
298B SER* 3.4 41.0 + - - -
373B ILE* 4.2 14.6 - - + -
374B SER 3.2 11.4 - - - +
375B PHE* 3.8 19.5 - + + -
386B SER* 4.6 1.6 + - - -
388B ASP* 2.9 46.6 + - + +
389B TYR* 3.4 39.7 - - - -
390B VAL* 4.1 15.3 - - + -
399B PHE 4.4 0.2 - - - -
400B ASP* 1.3 75.0 - - - +
402B LYS* 1.3 73.8 + - - +
403B VAL* 4.1 9.4 - - + -
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Residues in contact with LYS 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B PHE* 3.1 54.9 + - + +
153B SER* 4.2 10.3 - - - -
372B MET 3.7 0.5 - - - +
373B ILE* 3.2 6.6 - - - +
374B SER* 2.9 42.1 + - - +
386B SER* 6.4 1.1 - - - -
401B TYR* 1.3 82.1 - - - +
403B VAL* 1.3 63.8 + - - +
404B HIS* 4.1 19.1 - - - +
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Residues in contact with VAL 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B HIS* 3.1 48.0 + - + +
294B ALA 5.8 0.4 - - - +
298B SER* 4.1 24.5 - - - +
300B VAL* 3.9 20.2 - - + -
371B ILE* 3.9 14.4 - - + -
372B MET 3.4 1.1 - - - -
373B ILE* 3.4 34.5 - - + -
401B TYR* 4.1 9.9 - - + -
402B LYS* 1.3 73.4 - - - +
404B HIS* 1.3 73.2 + - - +
405B PHE* 6.1 0.2 - - + -
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Residues in contact with HIS 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LYS 4.6 11.0 - - - -
101B HIS* 3.4 14.4 + - - +
102B VAL 5.7 0.4 - - - -
103B ASP* 4.8 4.1 + - + -
149B HIS* 2.7 50.8 + + + +
371B ILE* 3.4 4.4 - - - -
372B MET* 2.7 45.8 + - + +
374B SER* 4.6 3.8 - - - -
402B LYS* 4.1 28.4 - - + +
403B VAL* 1.3 92.6 + - - +
405B PHE* 1.3 66.9 + - - +
406B ILE* 3.8 1.5 + - + -
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Residues in contact with PHE 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU* 3.9 22.7 - - + -
101B HIS* 3.0 36.0 + + + +
102B VAL* 4.0 15.3 - - + +
103B ASP 5.1 4.2 + - - +
149B HIS* 5.7 0.9 - - - -
300B VAL* 3.4 48.0 - - + -
301B LEU* 5.7 0.2 - - + -
303B ARG* 5.6 1.6 - - + -
304B LEU* 3.9 28.9 - - + -
369B CYS* 4.3 17.5 - - - -
370B SER 3.5 2.7 - - - +
371B ILE* 4.2 19.3 - - + -
404B HIS* 1.3 75.6 - - - +
406B ILE* 1.3 63.8 + - - +
408B LEU* 4.0 27.9 - - + +
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Residues in contact with ILE 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B LEU* 6.3 3.1 - - + -
149B HIS* 4.9 17.5 - - + +
166B GLU* 3.7 34.3 - - - +
369B CYS* 3.5 5.9 - - - +
370B SER* 2.8 40.8 + - - +
372B MET* 3.7 27.8 - - + -
404B HIS* 4.5 4.5 - - + +
405B PHE* 1.3 78.8 - - - +
407B ASP* 1.3 84.0 + - - +
408B LEU* 3.3 5.7 + - - +
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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