Contacts of the helix formed by residues 749 - 761 (chain A) in PDB entry 2VE8
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 LEU 749 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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747A ASP* 2.7 20.1 + - - +
748A PRO* 1.4 73.2 - - + +
750A TYR* 1.3 63.2 + - - +
751A ASP 3.3 2.2 - - - -
752A GLU* 3.2 4.8 + - + +
753A ALA* 2.9 21.7 + - - +
772A LEU* 4.4 11.2 - - + -
774A ILE* 4.2 14.4 - - + -
778A ARG* 3.5 31.2 - - - +
782A MET* 3.6 12.3 - - + -
749D LEU* 3.9 37.0 - - + -
752D GLU* 3.5 20.0 - - - +
772D LEU* 4.0 26.7 - - + +
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Residues in contact with TYR 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746A ASP* 6.0 0.9 - - - -
747A ASP* 3.2 20.2 + - + +
748A PRO 3.2 1.2 - - - -
749A LEU* 1.3 77.1 - - - +
751A ASP* 1.3 74.5 + - - +
753A ALA* 3.1 3.3 + - - +
754A VAL* 2.8 51.6 + - + +
782A MET* 3.6 23.9 - - + -
785A ALA* 3.8 28.3 - - + -
786A MET* 3.6 26.5 - - + -
789A ALA* 3.5 27.0 - - + +
791A VAL* 3.9 5.5 - - - +
762F ARG* 4.5 14.1 - - - +
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Residues in contact with ASP 751 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748A PRO 4.5 4.4 + - - +
749A LEU 3.3 0.4 - - - -
750A TYR* 1.3 94.0 - - - +
752A GLU* 1.3 58.2 + - - +
754A VAL* 3.2 7.3 + - - +
755A ARG* 2.9 50.4 + - - +
809C VAL* 3.6 24.6 - - + +
752D GLU* 5.7 2.7 - - - +
762F ARG* 3.1 33.2 + - - +
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Residues in contact with GLU 752 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749A LEU* 3.2 9.9 + - + +
751A ASP* 1.3 78.4 - - - +
753A ALA* 1.3 61.3 + - - +
755A ARG* 2.6 45.5 + - - +
756A PHE* 3.0 21.5 + - - +
771A LYS* 6.6 0.2 - - - -
772A LEU* 3.9 24.4 - - + +
748D PRO 4.3 12.2 - - - +
749D LEU* 4.8 2.5 - - + -
751D ASP* 5.2 3.1 - - - +
752D GLU* 2.8 41.7 + - + +
755D ARG* 3.4 9.9 + - - -
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Residues in contact with ALA 753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749A LEU 2.9 13.6 + - - +
750A TYR* 3.5 6.5 - - - +
752A GLU* 1.3 76.0 - - - +
754A VAL* 1.3 57.1 + - - +
756A PHE* 3.2 7.6 + - - +
757A VAL* 2.9 33.1 + - - +
768A VAL* 4.6 7.0 - - + -
772A LEU* 4.1 16.1 - - + +
782A MET* 3.9 18.2 - - + -
786A MET* 3.4 21.1 - - + -
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Residues in contact with VAL 754 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A TYR* 2.8 57.3 + - + +
751A ASP* 3.2 8.5 + - - +
753A ALA* 1.3 72.1 - - - +
755A ARG* 1.3 67.2 + - + +
757A VAL* 4.2 5.4 - - - -
758A THR* 2.8 43.7 + - + +
786A MET* 4.0 11.9 - - + -
791A VAL* 4.3 14.1 - - + -
805A ALA* 5.8 0.7 - - + -
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Residues in contact with ARG 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751A ASP* 2.9 24.5 + - - +
752A GLU* 2.6 51.9 + - - +
754A VAL* 1.3 77.1 - - + +
756A PHE* 1.4 57.8 + - - +
758A THR* 3.5 5.1 + - - -
759A GLU* 3.0 49.5 + - - +
808A PRO* 4.3 17.6 - - + +
809C VAL* 4.2 23.0 - - - +
752D GLU* 4.5 4.6 + - - -
755D ARG* 3.7 21.5 - - - +
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Residues in contact with PHE 756 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752A GLU 3.0 12.9 + - - +
753A ALA* 3.5 8.7 - - - +
755A ARG* 1.4 76.2 - - - +
757A VAL* 1.3 67.2 + - + +
759A GLU* 3.3 6.1 + - - -
760A SER* 2.9 52.1 + - - -
762A ARG* 4.0 10.5 - - + -
767A ALA* 3.7 44.0 - - + -
768A VAL* 4.1 11.2 - - + -
771A LYS* 3.5 42.0 - - + +
772A LEU* 5.7 2.0 - - + -
802G GLU* 3.5 35.2 - - + -
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Residues in contact with VAL 757 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753A ALA 2.9 18.5 + - - +
754A VAL* 3.7 8.7 - - - +
756A PHE* 1.3 84.3 - - + +
758A THR* 1.3 69.6 + - + +
760A SER* 3.8 0.2 - - - -
761A ARG* 2.8 31.4 + - - -
762A ARG 3.4 23.6 - - - +
763A ALA* 4.2 6.7 - - + -
768A VAL* 3.9 11.9 - - + -
783A ILE* 5.6 0.2 - - + -
786A MET* 3.7 34.8 - - + -
791A VAL* 4.2 7.0 - - + -
792A VAL* 4.5 2.7 - - + -
803A VAL* 3.6 14.1 - - + +
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Residues in contact with THR 758 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754A VAL* 2.8 41.5 + - + +
755A ARG* 3.5 1.4 + - - -
757A VAL* 1.3 81.7 - - + +
759A GLU* 1.3 61.1 + - - +
761A ARG* 2.9 32.2 + - - +
791A VAL* 4.1 1.6 - - + -
803A VAL* 4.1 8.1 - - + -
805A ALA* 3.9 23.6 - - + +
806A PRO 3.5 21.8 + - - +
807A ALA* 3.4 11.0 - - - +
808A PRO* 3.4 18.7 - - - +
798G ASN* 4.3 0.3 + - - -
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Residues in contact with GLU 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755A ARG* 3.0 34.2 + - - +
756A PHE* 3.9 4.6 - - - +
758A THR* 1.3 79.2 - - - +
760A SER* 1.3 59.3 + - - +
771A LYS* 6.2 0.3 - - - -
807A ALA* 4.5 2.9 - - + -
808A PRO* 3.5 31.0 - - + +
796G ASN* 2.9 18.4 - - - +
798G ASN* 3.0 21.0 + - - +
800G SER* 3.5 23.9 + - - +
802G GLU* 4.6 7.0 - - - +
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Residues in contact with SER 760 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756A PHE* 2.9 42.2 + - - -
759A GLU* 1.3 72.3 - - - +
761A ARG* 1.3 69.0 + - - +
762A ARG* 3.0 44.5 + - - +
796G ASN* 3.8 10.5 - - - +
800G SER* 5.1 0.7 - - - -
802G GLU* 3.6 27.8 - - - -
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Residues in contact with ARG 761 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757A VAL 2.8 12.2 + - - -
758A THR* 2.9 30.4 + - - +
760A SER* 1.3 82.7 - - - +
762A ARG* 1.4 61.3 + - - +
801A ARG 5.5 1.9 - - - +
802A GLU* 5.7 0.3 - - - -
803A VAL* 3.0 51.5 + - + +
804A ILE 3.8 3.2 + - - -
805A ALA 2.8 28.5 + - - -
807A ALA 3.8 6.9 - - - +
776E TYR* 3.4 67.3 - - + +
796G ASN* 4.4 2.9 - - - +
798G ASN* 3.9 6.5 - - - +
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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