Contacts of the helix formed by residues 736 - 748 (chain B) in PDB entry 2W3S
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 GLY 736 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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668B TYR* 4.2 9.7 + - - -
671B GLY* 3.8 4.5 - - - -
672B ALA* 3.4 29.7 - - - -
675B LEU* 3.7 12.2 - - - +
732B PRO 4.5 0.4 + - - -
733B PHE 3.2 6.1 + - - -
734B LEU 3.0 3.0 - - - -
735B LEU* 1.3 76.5 - - - +
737B ILE* 1.3 63.7 - - - +
739B ALA* 3.0 20.9 + - - +
740B PHE 3.6 2.4 + - - -
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Residues in contact with ILE 737 (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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347B PRO* 3.9 10.5 - - + +
350B ALA* 4.3 10.3 - - + -
351B LEU* 3.6 51.4 - - + +
354B GLU* 4.2 15.5 - - + -
451B SER* 3.7 12.3 - - - +
452B PRO 6.0 0.4 - - - +
674B TRP* 5.2 1.8 - - + -
675B LEU* 3.7 14.8 - - + +
734B LEU* 3.3 25.7 + - + +
736B GLY* 1.3 73.1 - - - +
738B SER* 1.3 67.7 + - - +
740B PHE* 2.7 17.0 + - - +
741B LEU* 2.9 31.4 + - + -
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Residues in contact with SER 738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ALA* 3.6 6.6 + - - +
451B SER* 2.8 29.2 + - - +
627B ALA* 3.5 22.0 + - - -
629B THR* 2.4 39.5 + - - -
735B LEU 3.0 19.9 + - - -
737B ILE* 1.3 71.0 - - - +
739B ALA* 1.3 59.0 + - - -
741B LEU* 4.0 3.1 - - - -
742B ALA* 3.2 23.4 + - - +
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Residues in contact with ALA 739 (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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629B THR* 3.4 23.3 + - + -
631B VAL* 4.7 2.9 - - + +
642B ILE* 4.4 9.0 - - + -
668B TYR* 4.0 4.3 - - - +
672B ALA* 3.9 22.9 - - + -
676B THR* 5.1 7.4 - - + -
736B GLY 3.0 12.5 + - - +
737B ILE 2.7 5.5 + - - -
738B SER* 1.3 73.8 - - - +
740B PHE* 1.3 64.0 + - - +
742B ALA* 3.1 4.3 + - - +
743B LEU* 3.0 27.3 + - + +
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Residues in contact with PHE 740 (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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166B PHE* 4.6 14.1 - + - -
351B LEU* 4.4 14.6 - - + -
355B ARG* 4.9 9.4 - - + -
675B LEU* 3.4 45.7 - - + +
676B THR* 5.7 0.2 - - - -
736B GLY 3.6 1.8 + - - -
737B ILE* 2.7 13.1 + - - +
739B ALA* 1.3 76.5 - - - +
741B LEU* 1.3 68.4 + - + +
743B LEU* 3.4 9.2 + - - +
744B HIS* 3.1 22.0 + - + +
757B LEU* 3.7 26.6 - - + +
758B GLN 3.4 34.8 - - - -
759B ALA* 3.7 17.3 - - + -
761B ALA* 3.6 16.6 - - + -
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Residues in contact with LEU 741 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B LEU* 5.4 2.7 - - + -
354B GLU* 4.3 15.7 - - + +
355B ARG* 5.1 7.2 - - + -
358B GLU* 3.7 31.8 - - + +
372B ARG* 3.3 23.6 - - - +
449B ALA* 3.4 17.7 - - + +
450B LEU 4.7 2.5 - - - +
451B SER* 3.8 15.0 - - - -
737B ILE* 2.9 34.3 + - + +
738B SER 3.9 1.3 - - - +
740B PHE* 1.3 90.9 - - + +
742B ALA* 1.3 56.2 + - - +
744B HIS* 3.3 13.8 + - + +
745B ASP* 2.9 25.5 + - - +
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Residues in contact with ALA 742 (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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447B GLY* 3.4 8.1 - - - -
448B ILE* 3.8 6.1 - - - -
449B ALA* 3.2 14.8 - - - +
629B THR* 3.3 32.8 - - - +
631B VAL* 3.6 12.0 - - + +
738B SER 3.2 14.1 + - - +
739B ALA 3.1 5.7 + - - +
741B LEU* 1.3 75.7 - - - +
743B LEU* 1.3 65.6 + - - +
745B ASP* 3.1 5.3 + - - +
746B ALA 3.0 18.4 + - - -
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Residues in contact with LEU 743 (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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631B VAL* 3.6 30.9 - - + +
633B ILE* 3.8 19.7 - - + +
640B ASN* 3.6 27.6 - - + +
641B ARG 5.4 0.2 - - - +
642B ILE* 6.6 0.2 - - + -
675B LEU 4.8 0.7 - - - +
676B THR* 3.9 20.6 - - + -
739B ALA* 3.0 12.9 + - + +
740B PHE* 3.5 11.2 - - - +
742B ALA* 1.3 77.3 - - - +
744B HIS* 1.3 61.5 + - - +
746B ALA* 3.1 15.5 + - - +
747B CYS* 3.3 14.6 + - - -
757B LEU* 4.2 7.2 - - + -
761B ALA* 3.8 26.0 - - + +
766B VAL* 4.1 12.6 - - + -
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Residues in contact with HIS 744 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B ARG* 6.0 2.4 + - - -
358B GLU* 3.6 19.3 - - + +
362B ARG* 3.0 33.3 + - - -
740B PHE* 3.1 17.6 + - + +
741B LEU* 3.6 15.3 - - + +
743B LEU* 1.3 76.3 - - - +
745B ASP* 1.3 60.3 + - - +
747B CYS* 3.4 8.0 + - - +
748B ALA* 3.0 26.4 + - + +
754B TRP* 3.4 38.1 - + - -
755B PRO* 4.0 22.3 - - + +
757B LEU* 3.7 26.3 + - + +
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Residues in contact with ASP 745 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B GLU* 5.6 0.9 - - - +
362B ARG* 3.3 29.7 + - - +
368B PRO* 6.0 0.9 - - - +
434B ILE* 5.5 2.1 - - - +
446B ARG 4.1 2.6 - - - +
447B GLY* 3.0 17.0 - - - -
448B ILE* 3.2 29.4 + - - +
449B ALA* 5.2 0.4 - - + -
741B LEU 2.9 13.1 + - - +
742B ALA 3.1 10.7 + - - +
744B HIS* 1.3 74.5 - - - +
746B ALA* 1.3 63.0 + - - +
748B ALA* 3.5 3.3 + - - +
749B ALA* 3.5 17.5 + - - +
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Residues in contact with ALA 746 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B ALA* 3.8 6.4 - - - +
446B ARG 3.8 7.9 - - - -
447B GLY* 3.4 25.9 - - - +
631B VAL* 4.6 2.9 - - + -
633B ILE* 3.7 32.4 - - + +
742B ALA 3.0 8.5 + - - +
743B LEU 3.1 10.2 + - - +
745B ASP* 1.3 75.1 - - - +
747B CYS* 1.3 61.2 + - - +
749B ALA* 3.1 16.2 + - - +
750B CYS* 3.4 12.5 - - - -
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Residues in contact with CYS 747 (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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633B ILE* 3.8 4.4 - - - +
743B LEU 3.3 12.7 + - - -
744B HIS* 3.4 11.2 - - - +
746B ALA* 1.3 71.6 - - - +
748B ALA* 1.3 52.8 + - - +
749B ALA 2.9 5.6 - - - -
750B CYS* 2.7 38.9 + - - +
755B PRO* 3.7 18.4 - - + -
757B LEU* 4.9 3.6 - - - -
766B VAL* 4.1 10.1 - - - -
769B ALA* 4.0 24.9 - - - +
770B VAL* 3.6 21.8 - - + -
773B ALA* 3.4 11.1 - - - +
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Residues in contact with ALA 748 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B ARG* 3.8 33.2 - - - +
744B HIS* 3.0 18.3 + - - +
745B ASP 3.9 3.4 - - - +
746B ALA 3.4 0.4 - - - -
747B CYS* 1.3 73.5 - - - +
749B ALA* 1.3 54.8 + - - +
750B CYS 3.4 1.6 - - - -
751B GLY 3.4 18.7 - - - +
753B HIS 5.0 2.2 - - - +
755B PRO* 3.7 18.5 - - + +
773B ALA* 4.8 1.3 - - - -
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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