Contacts of the helix formed by residues 736 - 749 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668D TYR* 3.9 16.5 + - - -
671D GLY 3.9 0.9 - - - -
672D ALA* 3.7 25.1 - - - -
675D LEU* 3.7 13.6 - - - +
732D PRO 4.2 0.4 + - - -
733D PHE 3.2 11.2 + - - -
734D LEU 3.1 2.6 - - - -
735D LEU* 1.3 77.8 - - - +
737D ILE* 1.3 61.0 + - - +
738D SER 3.2 0.4 - - - -
739D ALA* 3.1 19.9 + - - +
740D PHE 3.6 2.9 + - - -
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Residues in contact with ILE 737 (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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347D PRO* 4.0 7.6 - - + +
350D ALA* 4.4 10.3 - - + +
351D LEU* 3.9 50.7 - - + +
354D GLU* 4.3 13.7 - - + -
451D SER* 4.0 7.6 - - - +
674D TRP* 4.9 5.4 - - + -
675D LEU* 3.9 20.9 - - + -
733D PHE 5.8 0.2 - - - +
734D LEU* 3.1 27.4 + - + +
735D LEU 2.9 1.6 + - - -
736D GLY* 1.3 76.2 - - - +
738D SER* 1.3 64.5 + - - +
740D PHE* 3.1 3.5 + - + +
741D LEU* 3.0 39.1 + - + +
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Residues in contact with SER 738 (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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449D ALA* 3.7 14.0 - - - +
451D SER* 3.1 19.7 + - - -
627D ALA* 3.3 33.4 + - - +
629D THR* 3.0 22.4 + - - -
668D TYR* 4.0 0.2 - - - -
735D LEU 2.9 19.2 + - - -
737D ILE* 1.3 77.5 - - - +
739D ALA* 1.3 61.8 + - - +
741D LEU* 4.4 4.5 - - - -
742D ALA* 3.1 25.3 + - - +
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Residues in contact with ALA 739 (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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629D THR* 3.6 14.9 + - + -
631D VAL* 4.3 3.9 - - - +
642D ILE* 4.2 10.1 - - + -
668D TYR* 3.9 11.2 - - - +
672D ALA* 3.9 24.7 - - + -
675D LEU* 6.1 0.4 - - + -
676D THR* 5.1 6.3 - - + -
736D GLY 3.1 13.0 + - - +
737D ILE 3.1 0.6 - - - -
738D SER* 1.3 82.4 + - - +
740D PHE* 1.3 62.6 + - - +
742D ALA* 3.5 2.1 + - - +
743D LEU* 3.1 26.8 + - - +
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Residues in contact with PHE 740 (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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166D PHE* 4.7 4.5 - + - -
351D LEU* 4.3 14.1 - - + -
355D ARG* 4.6 20.0 - - + -
675D LEU* 3.8 45.2 - - + +
676D THR* 5.9 0.7 - - - -
736D GLY 3.6 1.6 + - - -
737D ILE* 3.1 8.2 + - + +
739D ALA* 1.3 78.9 - - - +
741D LEU* 1.3 70.4 + - + +
743D LEU* 3.3 10.0 + - - +
744D HIS* 2.9 27.8 + - + +
757D LEU* 3.5 42.7 - - + +
758D GLN 3.3 26.0 - - - -
759D ALA* 4.1 9.9 - - + -
761D ALA* 3.9 7.6 - - + -
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Residues in contact with LEU 741 (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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351D LEU* 5.4 1.1 - - + -
354D GLU* 4.2 17.3 - - + +
355D ARG* 5.1 4.7 - - + +
358D GLU* 4.1 19.2 - - + +
372D ARG* 3.3 32.3 - - - +
449D ALA* 3.5 15.5 - - + -
450D LEU 4.1 4.9 - - - +
451D SER* 3.7 27.8 - - - -
737D ILE* 3.0 25.3 + - + +
738D SER* 4.0 0.9 - - - +
740D PHE* 1.3 90.0 - - + +
742D ALA* 1.3 54.1 + - - +
744D HIS* 2.9 13.5 + - + +
745D ASP* 2.8 33.6 + - - +
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Residues in contact with ALA 742 (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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447D GLY* 3.4 22.3 - - - +
448D ILE 3.9 4.9 - - - -
449D ALA* 3.2 12.4 - - - +
629D THR 3.2 30.3 - - - +
631D VAL* 3.6 8.9 - - + +
738D SER 3.1 16.4 + - - +
739D ALA 3.9 3.6 - - - +
741D LEU* 1.3 75.6 - - - +
743D LEU* 1.3 57.4 + - - +
745D ASP* 3.2 0.4 + - - -
746D ALA* 2.8 25.8 + - - +
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Residues in contact with LEU 743 (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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631D VAL* 3.5 23.1 - - + +
633D ILE* 3.4 30.8 - - + +
640D ASN* 4.0 18.2 - - + +
641D ARG 6.2 0.2 - - - -
675D LEU 5.0 0.2 - - - +
676D THR* 4.1 20.9 - - + -
739D ALA 3.1 13.5 + - - +
740D PHE* 3.3 10.8 - - - +
742D ALA* 1.3 78.7 - - - +
744D HIS* 1.3 59.7 + - - +
746D ALA* 3.5 3.9 + - - +
747D CYS* 3.3 25.5 + - - -
757D LEU* 4.1 5.6 - - + +
761D ALA* 3.7 28.7 - - + +
766D VAL* 4.1 16.6 - - + +
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Residues in contact with HIS 744 (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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355D ARG* 6.0 2.7 - - - -
358D GLU* 3.1 38.6 + - + +
362D ARG* 3.4 19.8 + - + -
740D PHE* 2.9 17.3 + - + +
741D LEU* 2.9 14.6 + - + +
743D LEU* 1.3 75.3 - - - +
745D ASP* 1.3 60.1 + - - +
747D CYS* 3.2 8.5 - - - +
748D ALA* 2.9 24.6 + - + +
754D TRP* 3.2 39.3 - + - -
755D PRO* 3.9 19.0 - - + +
757D LEU* 3.8 23.7 + - + +
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Residues in contact with ASP 745 (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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358D GLU* 5.0 0.7 - - - +
362D ARG* 2.7 39.4 + - - +
434D ILE* 5.4 2.9 - - - +
446D ARG 4.5 1.2 - - - +
447D GLY* 3.3 6.8 - - - -
448D ILE* 3.1 39.8 + - - +
449D ALA* 5.1 0.9 - - + -
741D LEU 2.8 15.4 + - - +
742D ALA 3.2 7.6 + - - +
744D HIS* 1.3 70.4 - - + +
746D ALA* 1.3 65.4 + - - +
747D CYS 3.2 0.7 - - - -
748D ALA* 3.3 10.9 + - - +
749D ALA* 3.3 12.5 + - - +
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Residues in contact with ALA 746 (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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445D ALA* 3.7 4.3 - - - +
446D ARG 3.5 24.9 - - - +
447D GLY* 3.6 7.6 - - - +
631D VAL* 4.1 9.9 - - + -
633D ILE* 3.6 25.8 - - + +
742D ALA 2.8 16.7 + - - +
743D LEU 3.8 6.1 - - - +
744D HIS 3.3 0.2 - - - -
745D ASP* 1.3 77.3 - - - +
747D CYS* 1.3 59.4 + - - +
749D ALA* 3.6 8.9 + - - +
750D CYS* 3.6 14.9 - - - -
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Residues in contact with CYS 747 (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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633D ILE* 4.3 3.4 - - - -
743D LEU 3.3 16.9 + - - -
744D HIS* 3.2 13.6 + - - +
745D ASP 3.2 0.4 - - - -
746D ALA* 1.3 72.1 - - - +
748D ALA* 1.3 57.8 + - - +
749D ALA 2.9 4.9 - - - -
750D CYS* 2.8 25.5 + - - +
755D PRO* 3.7 16.8 - - + -
757D LEU* 5.1 3.1 - - - -
766D VAL* 3.7 13.7 - - - -
769D ALA* 3.7 29.4 - - - +
770D VAL* 3.7 21.5 - - - -
773D ALA* 3.4 15.5 - - - +
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Residues in contact with ALA 748 (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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362D ARG* 3.7 33.0 - - - +
744D HIS* 2.9 13.4 + - + +
745D ASP* 3.3 10.7 + - - +
747D CYS* 1.3 75.6 - - - +
749D ALA* 1.3 58.9 + - - +
750D CYS 3.3 0.2 - - - -
751D GLY 3.2 20.3 - - - +
753D HIS 5.1 0.9 - - - +
755D PRO* 3.8 15.8 - - + +
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Residues in contact with ALA 749 (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 ASN* 3.6 33.3 - - + +
445D ALA* 4.6 4.0 - - + -
446D ARG 4.5 1.8 - - - +
635D ARG* 4.7 4.8 + - - -
745D ASP 3.3 10.7 + - - +
746D ALA 3.7 12.3 - - - +
747D CYS 2.9 1.2 + - - -
748D ALA* 1.3 80.0 - - - +
750D CYS* 1.3 60.7 + - - +
751D GLY 3.3 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