Contacts of the helix formed by residues 718 - 727 (chain E) in PDB entry 6BAA
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 718 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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688E TRP* 4.3 11.7 - - - -
716E GLY* 3.1 5.9 - - - -
717E CYS* 1.3 80.0 - - - +
719E LYS* 1.3 56.3 + - - +
720E SER 3.3 2.5 - - - -
721E SER* 3.2 17.8 + - - -
722E LEU* 2.5 36.4 + - - +
903E MET* 5.5 2.7 - - - -
906E GLY* 4.8 5.8 - - - -
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Residues in contact with LYS 719 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711E ILE* 5.3 17.7 - - + +
712E VAL 5.7 5.4 - - - -
713E GLY 5.8 2.9 - - - +
714E GLN 5.7 4.7 - - - +
716E GLY 5.9 0.2 - - - +
717E CYS* 3.7 3.1 - - + +
718E GLY* 1.3 76.3 - - - +
720E SER* 1.3 58.6 + - - +
722E LEU* 3.1 11.0 + - - +
723E LEU* 2.9 26.5 + - - +
887E VAL* 5.5 6.1 - - + -
903E MET* 5.2 9.7 - - + +
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Residues in contact with SER 720 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688E TRP* 5.4 7.4 - - - -
718E GLY 3.3 0.4 - - - -
719E LYS* 1.3 78.2 - - - +
721E SER* 1.3 59.2 + - - +
723E LEU* 3.2 9.5 + - - +
724E LEU* 2.9 26.3 + - - +
775E GLN* 4.5 21.3 - - - -
854E ASP* 5.9 5.4 - - - -
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Residues in contact with SER 721 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686E PHE* 5.0 6.0 - - - +
687E THR 5.7 4.5 - - - -
688E TRP* 3.6 46.3 - - - -
695E THR* 6.1 2.0 - - - -
718E GLY* 3.2 12.0 + - - -
720E SER* 1.3 76.9 - - - +
722E LEU* 1.3 59.6 + - - +
724E LEU* 3.2 9.6 + - - +
725E ALA* 2.8 27.5 + - - +
730E MET* 5.2 1.7 - - - +
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Residues in contact with LEU 722 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718E GLY 2.5 20.4 + - - +
719E LYS* 3.1 11.2 + - - +
721E SER* 1.3 73.4 - - - +
723E LEU* 1.3 55.5 + - - +
725E ALA* 3.2 10.3 + - - +
726E THR* 2.9 25.8 + - - -
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Residues in contact with LEU 723 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719E LYS 2.9 12.4 + - - +
720E SER* 3.2 11.9 + - - +
722E LEU* 1.3 72.8 - - - +
724E LEU* 1.3 60.8 + - - +
726E THR* 3.1 10.9 + - - -
727E LEU* 2.9 26.3 + - - +
772E TYR* 4.9 21.0 - - + +
852E PHE* 6.0 5.4 - - + -
854E ASP* 5.3 10.8 - - + -
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Residues in contact with LEU 724 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720E SER 2.9 13.8 + - - +
721E SER* 3.2 13.0 + - - +
723E LEU* 1.3 72.1 - - - +
725E ALA* 1.3 57.6 + - - +
727E LEU* 3.1 5.6 + - - +
728E GLY 3.0 8.3 + - - -
729E GLU* 2.7 51.2 + - + +
730E MET* 4.4 2.7 - - + -
772E TYR* 5.8 1.7 + - - -
1212E THR* 6.1 2.0 - - + -
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Residues in contact with ALA 725 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686E PHE* 3.7 26.5 - - + -
721E SER 2.8 13.7 + - - +
722E LEU* 3.3 12.8 - - - +
724E LEU* 1.3 76.0 - - - +
726E THR* 1.3 63.1 + - - +
728E GLY* 3.1 12.2 + - - +
729E GLU 4.6 0.4 - - - +
730E MET* 4.3 10.5 - - + +
739E TRP* 3.2 14.3 - - - -
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Residues in contact with THR 726 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722E LEU 2.9 13.5 + - - -
723E LEU* 3.1 13.2 + - - -
725E ALA* 1.3 75.5 - - - +
727E LEU* 1.3 57.0 + - - +
739E TRP* 3.0 38.0 + - - +
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Residues in contact with LEU 727 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723E LEU 2.9 13.1 + - - +
724E LEU* 3.1 11.3 + - - +
726E THR* 1.3 76.7 - - - +
728E GLY* 1.3 62.3 + - - +
729E GLU* 3.5 6.9 + - + +
739E TRP* 5.0 2.2 - - - -
772E TYR* 5.6 7.9 - - + -
1212E THR* 4.8 11.2 - - + -
1216E ALA* 4.5 22.0 - - + +
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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