Contacts of the helix formed by residues 733 - 742 (chain J) in PDB entry 6ASX
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 733 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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726J ALA* 4.4 12.8 - - - +
732J GLY* 1.3 74.8 - - - -
734J ALA* 1.3 65.2 + - - +
735J ALA* 3.3 18.1 + - - +
736J GLN* 4.0 14.2 + - - +
737J ILE* 3.7 19.2 + - - +
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Residues in contact with ALA 734 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698J MET* 4.3 17.9 - - + +
726J ALA* 6.0 0.2 - - - -
733J SER* 1.3 76.0 - - - +
735J ALA* 1.3 61.1 + - - +
737J ILE* 3.3 10.5 - - - +
738J ARG* 2.9 41.9 + - - +
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Residues in contact with ALA 735 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733J SER* 3.3 10.1 + - - +
734J ALA* 1.3 80.1 - - - +
736J GLN* 1.3 60.3 + - + +
738J ARG* 3.3 22.0 - - - +
739J GLN* 2.9 38.2 + - - +
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Residues in contact with GLN 736 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104I PRO* 3.6 11.6 - - + +
1105I SER* 3.3 40.0 + - - -
1107I MET* 4.2 21.2 - - + +
732J GLY* 3.3 21.0 - - - -
733J SER* 3.8 15.3 + - - +
734J ALA 3.3 0.4 - - - -
735J ALA* 1.3 78.4 - - + +
737J ILE* 1.3 60.4 + - - +
739J GLN* 3.2 4.4 + - - +
740J LEU* 3.0 34.5 + - - +
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Residues in contact with ILE 737 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104I PRO* 6.5 0.2 - - + -
644J MET* 6.2 0.9 - - + -
697J MET* 3.3 9.7 - - + +
698J MET* 4.1 18.4 - - + -
701J LEU* 3.7 28.5 - - + -
722J ILE* 3.7 51.6 - - + +
723J TYR* 4.6 3.1 - - + +
726J ALA* 4.5 11.2 - - + -
733J SER 3.7 13.3 + - - +
734J ALA* 3.3 19.1 - - - +
736J GLN* 1.3 74.6 - - - +
738J ARG* 1.3 59.0 + - - +
740J LEU* 3.3 6.6 + - + +
741J ALA* 3.0 25.5 + - + +
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Residues in contact with ARG 738 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690J ASN* 4.7 12.3 - - - +
691J ASP* 5.2 7.5 + - - -
694J SER* 2.7 39.8 + - - +
695J LYS* 6.4 0.4 - - - +
697J MET* 3.7 15.5 - - + -
698J MET* 5.7 2.8 - - + +
734J ALA* 2.9 31.4 + - - +
735J ALA* 3.3 23.1 - - - +
736J GLN 3.2 0.2 - - - -
737J ILE* 1.3 78.1 - - - +
739J GLN* 1.3 60.2 + - + +
742J GLY* 2.9 33.3 + - - +
743J MET 4.1 11.4 - - - +
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Residues in contact with GLN 739 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107I MET* 3.3 33.8 - - - +
735J ALA* 2.9 24.8 + - - +
736J GLN* 3.2 8.5 + - - +
738J ARG* 1.3 79.7 - - + +
740J LEU* 1.3 60.5 + - - +
742J GLY 4.1 3.8 - - - +
744J ARG* 4.0 52.2 + - + +
747J MET* 5.6 4.0 - - - +
762J ASN* 4.0 6.4 - - - +
763J PHE* 3.7 23.2 + - + +
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Residues in contact with LEU 740 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1103I VAL 5.2 1.1 - - - +
1104I PRO* 4.5 14.4 - - + +
1107I MET* 3.7 35.0 - - + -
1109I ILE* 4.2 16.4 - - + -
644J MET* 3.7 34.4 - - + +
722J ILE* 3.7 21.1 - - + -
736J GLN 3.0 26.7 + - - +
737J ILE* 3.3 7.8 + - + +
738J ARG 3.2 0.2 - - - -
739J GLN* 1.3 79.9 - - - +
741J ALA* 1.3 59.5 + - - +
762J ASN* 4.5 3.8 - - - +
763J PHE* 4.5 16.6 - - + +
764J ARG* 4.1 22.3 + - - +
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Residues in contact with ALA 741 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644J MET* 5.4 4.3 - - + -
645J VAL 4.3 21.8 - - - +
646J ILE* 3.3 13.2 - - + +
647J PRO* 4.6 6.4 - - + +
650J LYS* 3.7 2.4 + - - -
697J MET* 3.6 20.9 - - + -
701J LEU* 5.6 3.6 - - + -
737J ILE* 3.0 15.8 + - + +
738J ARG 3.4 0.2 + - - -
740J LEU* 1.3 79.9 - - - +
742J GLY* 1.3 56.8 + - - +
762J ASN* 2.4 30.0 + - - +
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Residues in contact with GLY 742 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647J PRO* 5.7 0.9 - - - -
650J LYS* 4.0 7.0 - - - -
693J VAL* 3.8 20.4 - - - -
697J MET* 3.4 11.2 - - - -
738J ARG* 2.9 22.4 + - - +
739J GLN 4.1 1.9 - - - +
741J ALA* 1.3 75.1 - - - +
743J MET* 1.3 66.8 + - - -
744J ARG 3.7 0.5 + - - -
762J ASN* 3.3 17.5 - - - +
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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