Contacts of the strand formed by residues 474 - 481 (chain B) in PDB entry 2CXQ
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 THR 474 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B ASP 4.4 1.7 - - - +
57B LYS* 3.0 33.9 + - - +
58B ASN* 3.5 13.1 - - - +
404B CYS* 3.3 14.6 - - + +
406B PHE* 3.8 14.4 - - + -
433B THR* 3.4 25.9 + - + +
436B LEU* 3.7 30.1 - - + -
472B ARG* 3.8 6.3 + - + +
473B PRO* 1.3 80.1 - - - +
475B ASN* 1.3 67.5 + - - +
476B SER* 4.9 0.5 + - - -
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Residues in contact with ASN 475 (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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53B VAL* 5.8 0.7 - - + -
54B ASP 3.5 3.6 - - - +
55B TYR* 3.3 20.4 - - - +
58B ASN* 2.7 33.2 + - - -
320B LEU* 3.6 22.3 - - + +
323B LEU* 3.8 10.3 - - - +
336B HIS* 5.1 2.4 - - - -
404B CYS 2.9 6.8 + - - +
405B ASP* 2.9 29.1 - - + +
406B PHE* 2.9 29.4 + - - +
474B THR* 1.3 76.3 - - - +
476B SER* 1.3 61.6 + - - +
477B ILE* 4.8 7.4 - - + -
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Residues in contact with SER 476 (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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545A LEU* 3.9 34.5 - - - +
52B LEU 3.4 2.4 - - - +
54B ASP* 2.8 42.0 + - - +
57B LYS* 4.4 3.0 + - - -
406B PHE* 3.4 4.4 - - - +
429B PHE* 3.9 13.8 - - - -
433B THR* 3.7 27.0 + - - +
474B THR* 4.4 0.5 + - - -
475B ASN* 1.3 70.3 - - - +
477B ILE* 1.3 62.6 + - - +
478B VAL* 4.0 1.5 - - - +
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Residues in contact with ILE 477 (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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51B ILE* 4.2 9.0 - - + -
52B LEU 3.3 7.4 - - - +
53B VAL* 4.4 16.4 - - + -
320B LEU* 4.5 11.9 - - + -
405B ASP* 4.4 15.0 - - + +
406B PHE 2.7 12.5 + - - +
407B LEU* 3.2 16.9 - - + -
408B ILE 3.1 23.9 + - - -
475B ASN* 4.8 4.5 - - + -
476B SER* 1.3 76.3 - - - +
478B VAL* 1.3 62.2 + - - +
479B PHE* 3.6 6.7 - - + -
490B LEU* 4.0 26.9 - - + -
493B MET* 4.1 16.4 - - + -
494B TYR* 3.3 27.6 - - + +
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Residues in contact with VAL 478 (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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545A LEU* 3.7 31.0 - - + +
548A PHE* 3.5 19.6 - - + -
549A ILE* 4.6 10.3 - - + -
51B ILE* 3.5 1.4 - - - +
52B LEU* 2.7 40.1 + - + +
408B ILE* 3.4 18.6 - - + +
410B VAL* 3.6 25.1 - - + -
429B PHE* 3.8 23.8 - - + -
476B SER 4.5 0.7 - - - +
477B ILE* 1.3 78.3 - - - +
479B PHE* 1.3 63.3 + - - +
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Residues in contact with PHE 479 (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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548A PHE* 4.3 1.1 - - - -
50B HIS 3.2 12.8 - - - +
51B ILE* 4.1 7.2 - - + -
345B MET* 4.1 17.3 - - - -
407B LEU* 4.1 9.2 - - + -
408B ILE* 3.1 20.1 + - - -
409B PRO* 3.2 30.2 - - + +
410B VAL* 2.7 33.7 + - - -
477B ILE* 3.6 21.8 - - + -
478B VAL* 1.3 79.5 - - - +
480B THR* 1.3 57.1 + - - +
481B LYS 3.3 5.8 - - - -
482B LEU* 3.8 18.8 - - + -
486B ILE* 3.8 28.9 - - + -
490B LEU* 3.7 31.0 - - + -
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Residues in contact with THR 480 (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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548A PHE* 4.6 0.4 - - - -
552A GLN* 2.6 37.1 + - - +
555A THR* 4.2 7.2 - - - -
557A LEU* 3.7 24.2 - - + -
49B GLY* 3.6 3.1 - - - -
50B HIS 2.9 26.9 + - - -
410B VAL* 3.4 9.2 + - - +
411B GLN* 2.8 51.4 + - - +
479B PHE* 1.3 71.9 - - - +
481B LYS* 1.3 58.9 + - - +
486B ILE* 5.4 1.5 - - - +
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Residues in contact with LYS 481 (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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557A LEU* 4.2 26.0 - - + +
174B TYR* 4.1 4.3 - - - -
409B PRO* 4.0 7.2 - - - -
411B GLN* 3.8 32.7 + - + +
412B THR 4.6 12.6 + - - -
413B GLN* 3.5 34.4 + - - +
479B PHE* 3.2 6.1 + - - -
480B THR* 1.3 80.3 - - - +
482B LEU* 1.3 63.7 + - - +
483B THR* 3.1 24.7 + - + +
486B ILE* 3.4 23.4 - - - +
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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