Contacts of the helix formed by residues 736 - 749 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668H TYR* 3.6 19.2 + - - -
671H GLY 4.2 0.9 - - - -
672H ALA* 3.6 25.9 - - - -
675H LEU* 3.9 10.8 - - - +
732H PRO 4.2 0.2 + - - -
733H PHE 3.3 6.8 + - - -
734H LEU 3.1 2.0 - - - -
735H LEU* 1.3 73.7 - - - +
737H ILE* 1.3 65.2 + - - +
738H SER 3.1 0.9 - - - -
739H ALA* 3.1 20.1 + - - +
740H PHE 3.4 3.1 + - - -
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Residues in contact with ILE 737 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347H PRO* 4.1 8.3 - - + +
350H ALA* 4.5 6.5 - - + -
351H LEU* 4.0 38.6 - - + +
354H GLU* 4.0 20.9 - - + -
451H SER* 3.6 20.2 - - - +
674H TRP* 5.0 4.3 - - + -
675H LEU* 3.8 20.2 - - + -
733H PHE 4.8 0.2 + - - -
734H LEU* 3.1 30.4 + - + +
735H LEU 3.1 0.4 - - - -
736H GLY* 1.3 76.7 - - - +
738H SER* 1.3 64.8 + - - +
740H PHE* 2.9 5.2 + - - +
741H LEU* 2.8 34.3 + - + +
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Residues in contact with SER 738 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449H ALA* 3.8 12.5 - - - +
451H SER* 3.0 23.8 + - - +
627H ALA* 3.4 29.0 - - - +
629H THR* 2.5 26.7 + - - -
668H TYR* 3.9 0.7 - - - -
735H LEU 3.0 16.2 + - - -
737H ILE* 1.3 74.6 - - - +
739H ALA* 1.3 49.8 + - - +
741H LEU* 3.2 7.9 + - - +
742H ALA* 2.7 36.7 + - - +
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Residues in contact with ALA 739 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629H THR* 3.3 17.4 + - + -
631H VAL* 4.8 1.7 - - + +
642H ILE* 4.0 19.1 - - + -
668H TYR* 3.7 16.8 - - - +
672H ALA* 4.0 10.3 - - + -
676H THR* 5.0 4.9 - - + -
736H GLY 3.1 12.3 + - - +
738H SER* 1.3 81.0 + - - +
740H PHE* 1.3 58.0 + - - +
742H ALA* 3.0 3.1 + - - +
743H LEU* 2.8 34.6 + - + +
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Residues in contact with PHE 740 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166H PHE* 5.1 3.1 - + - -
351H LEU* 4.5 12.8 - - + -
355H ARG* 4.7 18.2 - - + -
675H LEU* 3.6 47.0 - - + +
676H THR* 5.5 0.4 - - - +
736H GLY 3.4 1.8 + - - -
737H ILE* 2.9 11.8 + - - +
739H ALA* 1.3 75.2 - - - +
741H LEU* 1.3 74.3 + - + +
743H LEU* 3.3 10.2 - - - +
744H HIS* 2.9 28.3 + - + +
757H LEU* 3.5 35.3 - - + +
758H GLN 3.8 1.8 - - - -
759H ALA* 3.6 28.0 - - + -
761H ALA* 3.7 21.8 - - + -
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Residues in contact with LEU 741 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351H LEU* 4.9 2.7 - - + -
354H GLU* 4.6 12.8 - - + +
355H ARG* 5.1 4.9 - - + +
358H GLU* 4.1 21.0 - - + +
372H ARG* 3.2 36.8 - - - +
449H ALA* 3.6 14.1 - - + +
450H LEU 4.7 2.5 - - - +
451H SER* 3.9 23.1 - - - -
737H ILE* 2.8 26.2 + - + +
738H SER* 3.6 7.2 - - - +
740H PHE* 1.3 90.7 - - + +
742H ALA* 1.3 49.5 + - - +
744H HIS* 3.1 13.0 + - + +
745H ASP* 2.8 33.6 + - - +
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Residues in contact with ALA 742 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447H GLY* 3.7 4.8 - - - +
448H ILE 4.2 0.2 - - - -
449H ALA* 3.3 13.9 - - - +
629H THR* 3.4 32.3 - - + +
631H VAL* 3.5 22.7 - - + +
738H SER 2.7 19.8 + - - +
739H ALA* 3.0 5.1 + - - +
741H LEU* 1.3 68.6 - - - +
743H LEU* 1.3 67.1 + - - +
745H ASP* 3.0 6.1 + - - +
746H ALA 3.0 19.6 + - - -
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Residues in contact with LEU 743 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631H VAL* 3.6 31.0 - - + +
633H ILE* 4.3 8.0 - - + +
640H ASN* 4.1 28.7 - - + +
641H ARG 5.9 0.2 - - - -
642H ILE* 6.1 1.1 - - + -
675H LEU 4.6 0.7 - - - +
676H THR* 3.8 26.0 - - + -
739H ALA* 2.8 14.6 + - + +
740H PHE* 3.3 11.7 - - - +
742H ALA* 1.3 74.0 - - - +
744H HIS* 1.3 62.8 + - - +
746H ALA* 3.2 10.8 + - - +
747H CYS* 3.2 15.5 + - - -
757H LEU* 3.9 9.6 - - + -
761H ALA* 3.7 29.2 - - + +
766H VAL* 4.3 13.0 - - + -
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Residues in contact with HIS 744 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355H ARG* 6.1 2.2 - - - -
358H GLU* 3.1 37.3 + - + +
362H ARG* 3.4 21.1 + - + -
740H PHE* 2.9 19.3 + - + +
741H LEU* 3.3 12.6 - - + +
743H LEU* 1.3 75.0 - - - +
745H ASP* 1.3 58.2 - - - +
747H CYS* 3.2 6.3 - - - +
748H ALA* 3.0 26.8 + - + +
754H TRP* 3.4 34.4 - + - -
755H PRO* 3.9 22.1 - - + +
757H LEU* 3.4 25.4 + - + +
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Residues in contact with ASP 745 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362H ARG* 2.9 36.7 + - - +
434H ILE* 5.3 2.1 - - - +
446H ARG 4.3 1.6 - - - +
447H GLY* 3.1 5.7 - - - -
448H ILE* 2.9 41.3 + - - +
449H ALA* 4.8 2.2 - - + -
741H LEU 2.8 15.5 + - - +
742H ALA 3.0 8.4 + - - +
744H HIS* 1.3 70.9 - - + +
746H ALA* 1.3 66.8 + - - +
748H ALA* 3.3 10.2 + - - +
749H ALA* 3.3 12.2 + - - +
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Residues in contact with ALA 746 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445H ALA* 4.2 4.9 - - - +
446H ARG 3.8 14.6 - - - -
447H GLY 3.7 18.6 - - - +
631H VAL* 4.5 3.8 - - + -
633H ILE* 3.8 31.0 - - + -
742H ALA 3.0 8.9 + - - +
743H LEU 3.4 9.6 - - - +
745H ASP* 1.3 76.5 + - - +
747H CYS* 1.3 63.6 + - - +
749H ALA* 2.9 20.7 + - - +
750H CYS* 3.8 5.0 + - - -
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Residues in contact with CYS 747 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633H ILE* 4.0 5.8 - - - +
743H LEU 3.2 13.8 + - - -
744H HIS* 3.2 13.9 - - - +
746H ALA* 1.3 77.6 - - - +
748H ALA* 1.3 56.1 + - - +
750H CYS* 2.8 32.9 + - - +
755H PRO* 3.7 18.2 - - + -
757H LEU* 4.5 4.9 - - - -
766H VAL* 4.0 21.8 - - - -
769H ALA* 4.0 26.0 - - - +
770H VAL* 4.0 10.1 - - - -
773H ALA* 3.3 9.3 - - - +
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Residues in contact with ALA 748 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362H ARG* 3.7 30.5 - - - +
744H HIS* 3.0 12.5 + - + +
745H ASP 3.3 9.3 + - - +
747H CYS* 1.3 78.2 - - - +
749H ALA* 1.3 55.4 + - - +
750H CYS 3.2 1.1 - - - -
751H GLY 3.1 22.4 - - - +
753H HIS 5.0 2.0 - - - +
755H PRO* 3.8 17.7 - - + +
773H ALA* 4.8 1.1 - - - -
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Residues in contact with ALA 749 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438H ASN* 3.5 32.6 + - + +
445H ALA* 5.2 2.0 - - + -
446H ARG 4.9 0.4 - - - +
635H ARG* 4.2 8.7 + - - -
745H ASP* 3.3 9.0 + - - +
746H ALA* 2.9 14.5 + - - +
747H CYS 2.9 0.6 + - - -
748H ALA* 1.3 75.7 - - - +
750H CYS* 1.3 58.7 + - - +
751H GLY 3.5 0.9 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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