Contacts of the helix formed by residues 700 - 718 (chain B) in PDB entry 1W7A
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 SER 700 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728A HIS* 3.2 23.9 + - - +
729A TYR* 5.7 0.2 - - - -
730A PHE* 5.0 10.5 - - - -
770A SER* 3.2 29.4 + - - -
699B THR* 1.3 83.0 + - - +
701B THR* 1.3 57.8 + - - +
702B TYR* 3.7 3.6 + - - +
703B ASP* 2.9 29.2 + - - +
704B GLY* 2.8 26.2 + - - -
729B TYR* 4.6 0.9 + - - -
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Residues in contact with THR 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A THR* 4.0 25.0 + - + +
702A TYR* 3.9 21.0 - - + +
705A LEU* 5.1 0.3 - - - +
728A HIS 4.7 0.6 + - - -
729A TYR* 4.0 17.1 - - - +
730A PHE 5.4 0.2 - - - +
731A GLU* 2.8 35.6 + - - +
699B THR 3.8 0.6 + - - -
700B SER* 1.3 72.3 - - - +
702B TYR* 1.3 68.2 + - + +
704B GLY* 3.8 0.2 - - - -
705B LEU* 2.8 36.6 + - + +
729B TYR* 4.2 10.8 + - + -
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Residues in contact with TYR 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A TYR* 4.1 20.0 + - - -
731A GLU* 5.5 2.7 - - - -
793A LEU* 3.6 17.5 - - + -
796A LEU* 3.7 56.0 + - + +
797A GLU* 4.6 14.1 - - + -
799A ILE* 4.2 14.5 - - + +
700B SER* 3.7 3.3 + - - +
701B THR* 1.3 85.8 - - + +
703B ASP* 1.3 65.2 + - - +
705B LEU* 3.9 4.3 - - + +
706B SER* 2.9 31.0 + - - -
799B ILE* 5.8 2.6 - - - +
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Residues in contact with ASP 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A SER* 2.9 31.6 + - - +
772A GLY* 2.7 34.2 + - - -
773A LEU* 3.5 17.5 + - + +
793A LEU* 3.9 22.2 - - - +
699B THR* 3.8 15.0 - - + +
700B SER* 2.9 12.9 + - - +
702B TYR* 1.3 74.6 - - - +
704B GLY* 1.3 58.4 + - - +
706B SER* 3.2 3.3 + - - -
707B LEU* 2.9 35.0 + - + +
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Residues in contact with GLY 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B GLY* 3.7 9.4 - - - -
699B THR* 3.4 14.5 - - - +
700B SER 2.8 18.4 + - - -
703B ASP* 1.3 73.8 - - - +
705B LEU* 1.3 62.5 + - - +
707B LEU* 3.4 5.4 + - - +
708B ALA* 3.0 23.9 + - - +
729B TYR* 3.1 20.8 + - - -
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Residues in contact with LEU 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A THR* 5.7 0.2 - - + -
792A LYS* 4.8 5.6 - - - -
796A LEU* 3.9 28.7 - - + -
701B THR* 2.8 26.2 + - + +
702B TYR* 3.9 8.1 - - + +
704B GLY* 1.3 73.4 - - - +
706B SER* 1.3 57.2 + - - +
708B ALA 3.8 0.2 - - - -
709B TRP* 2.9 33.0 + - + +
729B TYR* 3.3 30.0 + - + -
731B GLU* 4.0 37.9 - - + +
732B LEU* 3.7 25.1 - - + -
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Residues in contact with SER 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A LEU* 4.6 2.5 - - - -
789A ALA* 3.3 29.1 - - - +
792A LYS* 3.6 15.8 - - - +
793A LEU* 3.2 29.2 + - - +
796A LEU* 3.8 3.5 - - - +
702B TYR 2.9 23.1 + - - -
703B ASP* 3.6 5.8 - - - -
705B LEU* 1.3 75.8 - - - +
707B LEU* 1.3 61.7 + - - +
709B TRP* 3.8 1.7 - - - +
710B ALA* 3.1 26.0 + - - +
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Residues in contact with LEU 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A GLY 4.3 3.6 - - - +
773A LEU* 3.4 27.8 - - + -
776A ALA* 3.9 31.0 - - + -
781A VAL* 4.9 8.5 - - + -
785A VAL* 5.2 2.7 - - + -
786A ILE* 4.5 9.9 - - + -
789A ALA* 4.3 9.6 - - + -
670B PHE* 4.3 19.3 - - + -
674B MET* 4.3 12.3 - - + -
695B ILE* 5.1 5.8 - - + -
696B GLY* 5.7 1.3 - - - -
699B THR* 5.0 0.2 - - + -
703B ASP 2.9 17.0 + - - +
704B GLY* 3.7 7.4 - - - +
706B SER* 1.3 76.8 - - - +
708B ALA* 1.3 60.1 + - - +
710B ALA* 3.4 1.5 + - - +
711B CYS* 2.9 41.5 + - - -
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Residues in contact with ALA 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695B ILE* 3.6 24.9 - - - +
704B GLY 3.0 17.0 + - - +
705B LEU 3.9 2.2 - - - +
707B LEU* 1.3 74.1 - - - +
709B TRP* 1.3 67.4 + - - +
711B CYS* 4.5 1.8 - - - -
712B ALA* 2.9 26.9 + - - +
725B PHE* 3.6 15.2 - - + -
727B THR* 5.1 0.4 - - - +
729B TYR* 3.9 15.9 - - + -
732B LEU* 4.0 13.7 - - + -
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Residues in contact with TRP 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A ARG* 5.8 2.5 - - + -
792A LYS* 3.4 47.9 - - + +
705B LEU* 2.9 22.2 + - + +
706B SER 3.8 4.0 - - - +
708B ALA* 1.3 76.7 - - - +
710B ALA* 1.3 59.1 + - + +
712B ALA* 3.8 2.9 - - - +
713B GLU* 2.9 48.6 + - - +
731B GLU* 3.5 27.6 - - + -
732B LEU* 3.3 29.9 - - + +
734B GLN* 4.5 11.7 - - + -
735B LEU* 3.6 28.7 - - + +
738B LYS* 4.0 27.1 - - + -
739B MET* 5.1 0.8 - - + +
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Residues in contact with ALA 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A VAL* 3.7 34.0 - - + +
788A ARG* 4.0 13.3 - - + +
789A ALA* 3.8 13.0 - - + +
792A LYS* 6.0 0.4 - - + -
706B SER 3.1 19.5 + - - +
707B LEU 3.9 2.0 - - - +
709B TRP* 1.3 77.0 - - + +
711B CYS* 1.3 64.6 + - - +
713B GLU* 3.6 6.6 + - - +
714B ASN* 3.0 25.6 + - - +
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Residues in contact with CYS 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781A VAL* 5.4 2.5 - - - -
785A VAL* 4.1 11.9 - - - -
674B MET* 6.1 1.3 - - - -
677B THR* 3.9 15.3 - - - -
681B LEU* 3.8 29.0 - - + +
692B MET* 4.4 17.7 - - + -
695B ILE* 4.9 7.0 - - + -
707B LEU* 2.9 34.2 + - - +
708B ALA* 3.8 4.9 - - - +
710B ALA* 1.3 76.2 - - - +
712B ALA* 1.3 57.1 + - - +
714B ASN* 3.2 3.5 + - - +
715B LEU* 2.9 33.6 + - - +
725B PHE* 4.5 2.9 - - + -
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Residues in contact with ALA 712 (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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609B MET* 3.1 29.3 - - - +
708B ALA 2.9 18.0 + - - +
709B TRP 3.8 2.9 - - - +
711B CYS* 1.3 75.9 - - - +
713B GLU* 1.3 57.3 + - - +
715B LEU 3.3 0.2 + - - -
716B ALA* 3.0 26.9 + - - +
725B PHE* 3.9 22.1 - - + -
732B LEU* 4.6 0.2 - - + -
735B LEU* 3.8 24.2 - - + -
739B MET* 5.4 0.7 - - - -
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Residues in contact with GLU 713 (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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788A ARG* 2.8 58.7 + - - +
709B TRP* 2.9 37.2 + - + +
710B ALA 3.8 3.8 - - - +
712B ALA* 1.3 77.0 - - - +
714B ASN* 1.3 56.9 + - - +
716B ALA 3.3 0.3 + - - -
717B ASN* 2.9 46.1 + - + +
735B LEU* 5.2 1.4 - - + +
739B MET* 4.0 31.8 - - + +
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Residues in contact with ASN 714 (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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782A PRO* 6.1 0.2 - - - +
784A GLU* 5.2 7.1 - - - +
785A VAL* 3.9 24.1 - - + +
681B LEU* 3.6 14.6 + - + +
710B ALA 3.0 18.8 + - - +
711B CYS 3.6 3.6 - - - +
713B GLU* 1.3 76.5 + - - +
715B LEU* 1.3 60.3 + - - +
717B ASN* 5.5 0.2 - - - -
718B LYS* 3.1 29.6 + - - +
719B ILE* 2.9 53.2 + - - +
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Residues in contact with LEU 715 (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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609B MET* 3.5 18.8 - - + -
680B ILE* 4.4 6.3 - - + -
681B LEU* 3.9 12.6 - - + -
684B ALA* 4.9 0.2 - - + -
690B VAL* 3.9 30.3 - - + -
692B MET* 4.0 28.0 - - + -
711B CYS 2.9 20.2 + - - +
712B ALA 3.3 0.2 + - - -
714B ASN* 1.3 76.8 - - - +
716B ALA* 1.3 54.6 + - - +
719B ILE* 4.1 18.4 - - + -
720B LYS* 2.7 31.4 + - - -
721B ALA* 3.5 15.5 + - + +
723B THR* 3.8 23.6 - - + +
725B PHE* 4.5 2.2 - - + -
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Residues in contact with ALA 716 (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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608B ARG* 2.9 36.3 + - + +
609B MET* 3.9 13.2 - - + +
712B ALA 3.0 17.5 + - - +
713B GLU 3.9 1.8 - - - +
715B LEU* 1.3 78.1 - - - +
717B ASN* 1.3 66.8 + - - +
718B LYS 3.7 0.2 - - - -
720B LYS* 3.6 7.2 - - - +
721B ALA 5.7 1.8 - - - -
739B MET* 4.3 4.7 - - - -
741B GLY 5.6 0.4 - - - +
742B VAL* 3.8 28.5 - - + -
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Residues in contact with ASN 717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B ARG* 4.3 7.3 - - - +
713B GLU* 2.9 28.1 + - + +
716B ALA* 1.3 80.0 + - - +
718B LYS* 1.3 60.2 + - + +
720B LYS* 3.6 21.2 - - - +
739B MET* 3.7 40.2 - - - +
740B GLU 4.5 1.6 + - - +
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Residues in contact with LYS 718 (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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681B LEU 4.9 7.9 + - - -
714B ASN* 3.1 30.7 + - - +
717B ASN* 1.3 80.3 - - + +
719B ILE* 1.3 84.5 + - + +
720B LYS* 3.4 5.6 - - - +
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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