Contacts of the strand formed by residues 442 - 447 (chain B) in PDB entry 3WF4
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 442 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B VAL* 4.0 4.6 - - - +
440B HIS 3.9 0.2 - - - -
441B ASP* 1.3 80.3 + - - +
443B ALA* 1.3 61.9 + - - +
444B TYR* 3.2 25.0 + - + +
454B VAL* 3.8 12.9 - - + +
455B LEU 3.2 11.9 - - - +
456B GLU* 3.0 43.7 + - - +
476B LEU 3.7 0.7 - - - +
477B VAL* 3.3 4.7 - - - +
478B GLU* 3.0 30.8 + - + +
480B MET* 3.8 23.8 - - - -
578B LYS* 3.9 7.0 - - - +
592B TRP* 3.8 26.5 - - - +
595B ARG* 5.3 2.0 - - - +
622B GLU* 3.0 33.5 + - - -
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Residues in contact with ALA 443 (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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439B VAL* 3.9 16.4 - - + +
442B ARG* 1.3 75.2 - - - +
444B TYR* 1.3 63.5 + - - +
445B VAL* 3.8 2.7 + - + +
454B VAL* 3.3 9.7 - - - +
455B LEU* 2.8 37.8 + - + +
475B LEU* 4.1 27.6 - - + -
476B LEU 3.2 6.7 - - - +
477B VAL* 4.2 9.9 - - + -
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Residues in contact with TYR 444 (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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415B PHE* 4.8 0.7 - + - -
442B ARG* 3.2 31.4 - - + -
443B ALA* 1.3 73.1 - - - +
445B VAL* 1.3 61.3 + - - +
446B ALA* 4.1 0.5 + - - +
453B GLY 4.0 4.0 - - - +
454B VAL* 4.2 7.9 - - + -
474B ASP* 3.9 1.7 - - - +
475B LEU* 3.8 1.0 - - - -
476B LEU* 2.9 48.0 + - + +
478B GLU* 2.7 39.3 + - + -
549B PRO* 3.9 17.7 - - + +
578B LYS* 3.5 9.9 - - + +
621B LEU* 3.5 51.8 - - + +
622B GLU* 3.4 31.2 - - + -
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Residues in contact with VAL 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B LEU* 4.0 10.8 - - + -
443B ALA 4.2 8.7 - - - +
444B TYR* 1.3 75.0 - - - +
446B ALA* 1.3 60.1 + - - +
451B PRO* 3.4 5.4 - - - +
452B GLN* 2.7 45.9 + - + -
453B GLY 3.0 16.5 + - - +
455B LEU* 4.3 10.1 - - + +
463B LEU* 3.9 19.5 - - + -
465B ILE* 4.3 1.6 - - + -
473B LEU* 4.0 20.2 - - + -
474B ASP 3.5 8.7 - - - +
475B LEU* 3.8 26.2 - - + -
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Residues in contact with ALA 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B TYR 4.1 0.8 + - - +
445B VAL* 1.3 75.8 - - - +
447B VAL* 1.3 67.4 + - - +
449B GLY 4.6 4.0 - - - +
450B ILE 3.2 17.0 - - - +
451B PRO 4.1 0.2 - - - -
452B GLN* 4.1 1.3 - - - -
472B THR 3.6 1.2 - - - +
473B LEU* 3.6 1.7 - - - +
474B ASP* 3.0 44.0 + - + +
548B LEU* 3.6 29.6 - - + -
549B PRO* 5.9 0.7 - - + -
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Residues in contact with VAL 447 (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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422B LEU* 4.1 8.1 - - + -
446B ALA* 1.3 77.0 - - - +
448B ASP* 1.3 71.5 + - + +
450B ILE* 3.0 26.1 + - - +
452B GLN* 3.8 16.6 + - + +
465B ILE* 4.3 13.2 - - + -
466B THR 3.6 27.1 - - - +
467B GLY* 4.1 7.6 - - - -
471B ALA* 3.8 25.4 - - + -
472B THR 3.3 6.1 - - - +
473B LEU* 3.9 20.2 - - + -
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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