Contacts of the strand formed by residues 930 - 935 (chain I) 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 ASP 930 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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873I ILE* 5.1 6.1 - - - +
928I VAL* 3.5 3.0 + - - +
929I ILE* 1.3 90.8 - - + +
931I VAL* 1.3 71.3 + - - +
932I GLN* 3.0 29.6 + - - -
1052I VAL* 3.8 0.2 - - - -
1053I TYR* 3.0 49.5 + - + -
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Residues in contact with VAL 931 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870I ILE* 3.8 24.2 - - + -
871I VAL* 4.2 7.9 - - + +
872I TYR 5.1 0.2 - - - +
873I ILE* 4.9 9.6 - - + +
928I VAL* 4.0 18.8 - - + -
930I ASP* 1.3 84.0 + - - +
932I GLN* 1.3 75.0 + - - +
933I VAL* 4.1 11.4 + - + -
944I ARG* 3.9 21.8 - - - +
948I ILE* 4.1 25.1 - - + +
952I GLN* 5.7 1.0 + - - -
1050I VAL* 4.2 2.9 - - + -
1051I LYS 3.4 6.3 - - - +
1052I VAL* 4.5 7.4 - - + -
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Residues in contact with GLN 932 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87I ILE* 3.4 39.7 - - + +
930I ASP* 3.0 21.8 + - - -
931I VAL* 1.3 77.3 + - - +
933I VAL* 1.3 65.6 + - - +
934I PHE* 4.1 18.1 - - + -
948I ILE* 6.0 0.4 - - - -
952I GLN* 4.7 15.7 + - - +
1049I ILE 4.6 0.4 - - - -
1050I VAL* 3.6 1.2 - - - -
1051I LYS* 2.9 50.9 + - + +
1053I TYR* 3.9 25.1 - - + +
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Residues in contact with VAL 933 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870I ILE* 5.4 8.1 - - + -
931I VAL* 4.1 8.2 + - + -
932I GLN* 1.3 80.8 + - - +
934I PHE* 1.3 74.6 + - - +
935I THR* 3.9 14.2 + - - +
942I ASP* 5.4 0.9 - - - +
944I ARG* 5.8 0.9 - - + -
945I ALA* 3.8 29.4 - - + +
948I ILE* 4.0 28.3 - - + +
1040I ASP* 5.4 0.2 - - - +
1048I LYS* 5.2 7.6 - - + -
1049I ILE 3.6 4.9 - - - +
1050I VAL* 4.4 17.9 - - + -
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Residues in contact with PHE 934 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87I ILE* 3.4 29.8 - - + -
88I ARG* 3.9 28.5 - - + -
932I GLN* 4.1 24.0 - - + -
933I VAL* 1.3 84.8 - - - +
935I THR* 1.3 64.1 + - - +
1040I ASP* 3.9 22.0 - - + +
1042I LEU* 4.2 24.5 - - + -
1048I LYS* 3.2 7.8 - - - +
1049I ILE* 2.9 46.4 + - + +
1051I LYS* 4.3 26.5 - - + -
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Residues in contact with THR 935 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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933I VAL* 3.9 14.2 + - - +
934I PHE* 1.3 78.5 + - - +
936I ARG* 1.3 76.0 + - - +
937I ASP 3.6 0.2 + - - -
939I VAL* 3.7 28.5 - - + +
940I GLU 5.2 0.7 - - - +
941I LYS* 4.4 30.8 - - + +
945I ALA* 5.0 1.7 - - - +
1039I GLY* 4.3 3.6 - - - -
1040I ASP* 3.5 26.2 + - - +
1042I LEU* 4.1 4.9 - - - +
1047I LEU 4.0 4.7 - - - +
1048I LYS* 4.2 11.8 + - + +
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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