Contacts of the strand formed by residues 1034 - 1038 (chain J) in PDB entry 6ALG
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 PHE1034 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1033J GLY* 1.3 75.8 - - - -
1035J VAL* 1.3 62.5 + - - +
1036J ARG* 4.0 1.6 - - + -
1080J ILE* 3.6 4.5 - - - +
1081J VAL* 2.5 42.9 + - + +
1082J ASP* 3.6 18.1 - - - +
1083J ALA* 3.7 28.7 - - + -
1111J ASP* 5.6 1.1 - - - +
1112J GLY* 3.3 32.5 - - - +
1113J VAL 4.1 1.1 - - - -
1114J GLN* 3.6 35.0 - - + +
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Residues in contact with VAL1035 (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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1033J GLY 4.6 0.2 - - - +
1034J PHE* 1.3 78.0 - - - +
1036J ARG* 1.3 64.0 + - - +
1037J PHE* 3.7 9.2 + - + -
1078J LEU* 3.7 45.5 - - + -
1079J LYS 4.2 4.9 - - - +
1080J ILE* 3.7 13.2 - - + -
1109J LEU 5.6 3.8 - - - +
1110J GLU 5.3 4.5 - - - +
1111J ASP* 2.9 28.5 + - - +
1112J GLY 5.4 1.2 - - - +
1113J VAL 4.6 7.3 + - - +
1115J ILE* 3.7 32.1 - - + -
1121J LEU* 3.8 11.0 - - + -
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Residues in contact with ARG1036 (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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1034J PHE* 4.0 1.9 - - + -
1035J VAL* 1.3 76.0 - - - +
1037J PHE* 1.3 62.1 + - - +
1038J THR* 2.9 29.0 + - + +
1077J ALA 3.9 1.4 - - - +
1079J LYS* 3.5 38.5 + - - +
1081J VAL* 3.4 31.4 - - + +
1085J GLY* 4.4 12.2 + - - -
1087J ASP* 3.1 26.1 + - - -
1111J ASP* 4.3 7.0 - - - +
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Residues in contact with PHE1037 (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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1035J VAL* 3.7 11.8 + - + -
1036J ARG* 1.3 69.6 - - - +
1038J THR* 1.3 63.3 + - - +
1039J ASP 3.4 3.1 + - - -
1040J MET* 3.6 31.7 + - + +
1046J ILE* 5.5 0.9 - - + -
1059J LEU* 3.6 25.4 - - + -
1077J ALA 4.3 0.4 - - - -
1078J LEU* 3.6 25.6 - - + -
1107J VAL* 4.1 18.2 - - + -
1109J LEU 4.4 2.0 - - - -
1110J GLU* 3.6 14.4 - - + -
1111J ASP* 3.3 48.6 + - + +
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Residues in contact with THR1038 (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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1036J ARG* 2.9 38.1 + - + +
1037J PHE* 1.3 68.8 - - - +
1039J ASP* 1.3 67.8 + - - +
1040J MET* 3.9 0.5 - - - +
1075J ARG 3.8 0.5 - - - +
1077J ALA* 2.5 58.1 + - - +
1079J LYS* 4.1 28.1 + - + +
1098J GLN* 5.5 1.0 - - - +
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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