Contacts of the helix formed by residues 758 - 767 (chain B) in PDB entry 1IVS
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 ASN 758 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604B THR* 4.6 6.1 - - - -
605B LEU* 3.6 45.1 + - - +
606B ALA 4.9 0.5 + - - -
722B LEU* 4.5 10.3 - - + +
754B PRO* 3.1 19.0 + - - +
755B VAL 3.3 4.7 - - - +
757B GLU* 1.3 86.1 + - - +
759B LEU* 1.3 63.0 + - - +
760B GLU 3.5 1.8 - - - -
761B VAL* 3.0 32.0 + - + +
762B PHE* 3.1 10.7 + - - +
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Residues in contact with LEU 759 (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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755B VAL 2.9 15.5 + - - +
756B GLU* 3.2 16.4 - - - +
757B GLU 3.1 4.7 + - - +
758B ASN* 1.3 74.4 - - - +
760B GLU* 1.3 68.8 + - + +
762B PHE* 2.9 21.7 + - + +
763B ARG* 2.9 57.4 + - - +
770B LEU* 4.0 24.7 - - + -
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Residues in contact with GLU 760 (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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655B PRO* 4.1 20.3 - - + +
758B ASN 3.5 0.8 - - - -
759B LEU* 1.3 82.1 - - + +
761B VAL* 1.3 65.0 + - + +
763B ARG* 3.0 36.1 - - - +
764B PHE* 3.1 18.2 + - - +
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Residues in contact with VAL 761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B THR* 6.4 2.0 - - - -
606B ALA* 6.0 2.5 - - + -
652B ALA* 3.5 37.2 - - + +
655B PRO* 4.5 15.3 - - + -
656B ALA* 5.6 3.4 - - + +
719B PHE* 5.9 0.9 - - + -
722B LEU* 4.4 11.7 - - + -
758B ASN* 3.0 27.2 + - + +
760B GLU* 1.3 78.0 - - + +
762B PHE* 1.3 64.7 + - - +
764B PHE* 3.1 4.2 + - - +
765B LEU* 3.1 43.3 + - + +
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Residues in contact with PHE 762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B LEU* 4.8 3.4 - - + -
725B ALA* 4.6 1.6 - - + -
726B VAL* 3.6 26.5 - - + -
729B VAL* 4.0 24.9 - - + -
746B VAL* 5.7 3.8 - - + -
748B LEU* 4.6 6.7 - - + -
755B VAL* 3.3 38.4 - - + +
758B ASN 3.1 6.3 + - - +
759B LEU* 2.9 19.9 + - + +
761B VAL* 1.3 82.9 - - - +
763B ARG* 1.3 54.0 + - - +
765B LEU* 3.2 2.1 + - - +
766B SER* 2.5 59.2 + - - -
768B ALA* 3.9 19.1 - - + -
769B ASP 4.8 0.9 - - - -
770B LEU* 4.0 28.5 - - + -
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Residues in contact with ARG 763 (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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743B GLU* 4.7 6.9 + - - +
759B LEU* 2.9 41.0 + - - +
760B GLU* 3.0 41.1 - - - +
762B PHE* 1.3 78.9 - - + +
764B PHE* 1.3 56.5 + - - +
766B SER* 3.5 0.4 - - - -
767B ARG* 2.8 30.3 + - - -
768B ALA 3.4 24.0 + - - +
769B ASP* 3.0 41.4 + - - -
770B LEU* 3.5 23.4 + - - +
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Residues in contact with PHE 764 (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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651B GLU* 3.6 30.3 - - - -
652B ALA* 5.5 0.2 - - - -
654B LYS* 3.8 26.9 - - + -
655B PRO* 3.6 25.4 - - + -
658B LYS* 4.9 13.2 - - - -
760B GLU* 3.1 20.9 + - - +
761B VAL 3.1 7.2 + - - +
763B ARG* 1.3 78.4 - - - +
765B LEU* 1.3 74.9 + - + +
767B ARG* 2.8 56.8 + - - +
932D U 4.8 9.6 - - - -
933D C 5.6 4.3 - + - -
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Residues in contact with LEU 765 (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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647B ASP 5.7 0.4 - - - +
648B TRP* 4.1 26.2 - - + -
651B GLU* 3.8 33.2 - - + -
652B ALA* 4.6 5.6 - - + -
719B PHE* 6.1 0.2 - - + -
722B LEU* 4.4 3.6 - - + -
726B VAL* 3.6 15.5 - - + -
730B ARG* 2.6 36.7 + - - +
761B VAL* 3.1 34.9 + - + +
762B PHE 3.9 1.3 - - - +
764B PHE* 1.3 95.0 - - + +
766B SER* 1.3 61.5 + - - +
767B ARG* 4.7 3.1 - - - +
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Residues in contact with SER 766 (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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726B VAL* 4.0 5.6 - - - +
729B VAL* 3.8 20.1 - - - +
730B ARG* 3.6 13.7 - - - +
733B LYS* 3.6 16.8 - - - +
740B PRO 4.9 0.2 - - - +
762B PHE* 2.5 53.3 + - - -
763B ARG* 3.5 1.0 - - - -
765B LEU* 1.3 75.7 - - - +
767B ARG* 1.3 72.7 + - - +
768B ALA 3.4 9.1 + - - -
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Residues in contact with ARG 767 (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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733B LYS* 3.6 13.9 - - - -
740B PRO 3.2 28.0 - - - +
741B ALA* 3.8 10.0 + - - +
742B GLN 3.7 5.5 - - - +
743B GLU* 3.5 28.2 + - - +
744B VAL 3.7 2.8 + - - -
763B ARG 2.8 18.0 + - - -
764B PHE* 2.8 54.4 + - - +
765B LEU 3.5 3.2 - - - +
766B SER* 1.3 83.3 - - - +
768B ALA* 1.3 61.3 + - - +
932D U 3.0 37.7 + - - +
933D C 4.6 12.3 - - - +
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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