Contacts of the strand formed by residues 437 - 441 (chain D) in PDB entry 2W5E
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 437 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434D PRO* 3.1 21.6 + - + +
436D ALA* 1.3 81.9 - - - +
438D CYS* 1.3 60.5 + - - +
448D THR* 3.9 11.7 - - + -
449D GLY 3.5 3.4 - - - +
450D PHE* 4.2 2.9 - - + -
451D PHE* 4.1 1.8 - - - -
473D TYR* 3.3 23.7 - - - -
519D MET* 3.9 20.0 - - + +
520D ALA* 4.0 13.7 - - - +
521D TYR* 3.7 21.8 + - + +
526D LEU* 3.6 31.2 - - + -
554D PRO* 3.5 39.7 - - + -
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Residues in contact with CYS 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437D LEU* 1.3 75.2 - - - +
439D VAL* 1.3 67.1 + - - +
440D ILE* 4.1 4.0 - - - -
448D THR* 3.7 8.8 - - - +
449D GLY* 3.0 36.1 + - - +
451D PHE* 3.9 22.7 - - + -
456D ILE* 3.7 29.8 - - - -
471D VAL* 3.9 18.6 - - + -
472D CYS 3.5 14.1 - - - +
473D TYR* 4.1 3.6 - - + -
521D TYR* 3.9 6.3 - - - -
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Residues in contact with VAL 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-6C HIS* 3.5 36.3 - - + +
1591C CL 4.7 1.1 - - + -
438D CYS* 1.3 79.7 - - - +
440D ILE* 1.3 69.3 + - - +
441D ASP* 4.0 0.5 + - - +
446D LYS* 4.3 11.2 - - + -
447D GLY 3.5 11.4 - - - +
470D ASN 3.8 0.2 - - - +
471D VAL* 3.4 4.2 - - - +
472D CYS* 2.7 43.3 + - + +
521D TYR* 3.6 28.0 - - + -
1587D CL 3.6 20.6 - - + -
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Residues in contact with ILE 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438D CYS* 4.1 6.3 - - - -
439D VAL* 1.3 74.9 - - - +
441D ASP* 1.3 62.4 + - - +
442D THR* 4.6 3.4 - - + -
445D GLY 4.1 0.3 - - - +
446D LYS* 3.2 8.1 - - - +
447D GLY 2.8 33.4 + - - +
448D THR 4.3 3.4 - - - +
449D GLY* 4.0 19.1 - - - +
456D ILE* 3.8 28.7 - - + -
458D THR* 4.4 8.3 - - - +
462D VAL* 3.9 20.9 - - + +
463D VAL* 5.2 2.2 - - + -
469D VAL* 4.0 25.4 - - + -
470D ASN 3.4 6.1 - - - +
471D VAL* 3.9 19.5 - - + -
493D ILE* 3.9 12.3 - - + -
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Residues in contact with ASP 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439D VAL 5.2 0.2 - - - +
440D ILE* 1.3 74.0 - - - +
442D THR* 1.3 82.0 + - - +
445D GLY 3.8 1.7 - - - +
446D LYS* 2.8 37.6 + - - +
469D VAL* 4.0 1.0 - - - +
470D ASN* 2.7 66.9 + - + +
477D MET* 4.2 8.8 - - + +
1587D CL 4.2 10.5 - - + -
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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