Contacts of the strand formed by residues 442 - 447 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439D VAL* 4.0 4.5 - - - +
440D HIS 3.9 0.6 - - - -
441D ASP* 1.3 83.2 - - - +
443D ALA* 1.3 64.4 + - - +
444D TYR* 3.0 30.1 + - + +
454D VAL* 3.8 14.9 - - + +
455D LEU 3.3 12.3 - - - +
456D GLU* 3.4 36.4 + - - +
476D LEU 3.6 1.0 - - - +
477D VAL* 3.4 3.3 - - - +
478D GLU* 3.0 30.0 + - - +
480D MET* 3.9 17.6 - - + -
578D LYS* 3.7 13.5 - - - +
592D TRP* 3.7 28.9 - - - +
595D ARG* 4.1 4.2 - - - +
622D GLU* 2.6 33.5 + - - -
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Residues in contact with ALA 443 (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* 3.7 18.8 - - + -
442D ARG* 1.3 75.2 - - - +
444D TYR* 1.3 65.5 + - - +
445D VAL* 3.8 2.4 + - + +
454D VAL* 3.2 10.7 - - - +
455D LEU* 2.9 36.7 + - + -
475D LEU* 4.0 27.6 - - + -
476D LEU 3.3 3.6 - - - +
477D VAL* 4.0 11.4 - - + -
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Residues in contact with TYR 444 (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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442D ARG* 3.0 36.2 - - + -
443D ALA* 1.3 71.3 - - - +
445D VAL* 1.3 61.8 + - - +
446D ALA* 3.9 0.7 + - - +
453D GLY 3.9 3.4 - - - -
454D VAL* 3.8 15.5 - - + -
474D ASP* 3.6 3.6 - - - +
475D LEU* 3.6 0.2 - - - -
476D LEU* 2.8 54.2 + - + +
478D GLU* 2.6 39.6 + - + -
549D PRO* 3.9 24.4 - - + +
578D LYS* 3.3 9.1 - - + +
621D LEU* 3.3 53.1 - - + +
622D GLU* 3.8 15.3 - - + -
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Residues in contact with VAL 445 (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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432D LEU* 4.1 12.1 - - + -
443D ALA 4.1 8.7 - - - +
444D TYR* 1.3 76.6 - - - +
446D ALA* 1.3 64.9 + - - +
451D PRO* 3.6 4.0 - - - +
452D GLN* 2.9 39.8 + - + -
453D GLY 3.1 14.7 + - - +
455D LEU* 4.4 6.5 - - + -
463D LEU* 3.9 20.4 - - + -
465D ILE* 4.5 3.4 - - + -
473D LEU* 3.7 27.6 - - + -
474D ASP 3.2 4.7 - - - +
475D LEU* 4.1 22.2 - - + -
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Residues in contact with ALA 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444D TYR 3.9 1.1 + - - +
445D VAL* 1.3 75.8 - - - +
447D VAL* 1.3 65.3 + - - +
448D ASP 4.1 0.4 - - - -
449D GLY* 4.6 3.4 - - - +
450D ILE 3.4 15.0 - - - +
451D PRO* 4.2 1.3 - - + -
452D GLN* 4.1 0.4 - - - -
472D THR 3.7 1.0 - - - +
473D LEU* 3.7 2.3 - - - +
474D ASP* 2.9 43.6 + - + +
548D LEU* 3.6 31.2 - - + -
549D PRO* 5.9 2.7 - - + -
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Residues in contact with VAL 447 (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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422D LEU* 4.1 6.3 - - + -
446D ALA* 1.3 75.2 - - - +
448D ASP* 1.3 73.0 + - + +
449D GLY 3.4 0.4 - - - -
450D ILE* 3.0 26.2 + - - +
452D GLN* 3.7 17.4 + - + +
465D ILE* 4.1 15.5 - - + -
466D THR 3.2 27.6 - - - +
467D GLY* 4.0 7.4 - - - -
471D ALA* 3.9 24.5 - - + -
472D THR 3.3 5.4 - - - +
473D LEU* 3.9 22.2 - - + -
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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