Contacts of the strand formed by residues 1073 - 1077 (chain G) in PDB entry 5HZN
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 LEU1073 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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993G ARG* 3.4 25.1 - - + +
996G ILE* 4.6 13.9 - - + -
998G MET* 4.4 10.1 - - + -
1029G ILE* 4.0 20.9 - - + -
1030G LYS 3.3 7.6 - - - +
1031G THR* 3.8 26.0 - - + -
1044G PHE* 4.1 4.4 - - - -
1065G VAL* 3.9 2.4 - - - +
1066G VAL* 3.1 55.5 + - + +
1071G PRO* 3.4 26.7 - - + +
1072G THR* 1.3 74.3 - - - +
1074G VAL* 1.3 67.6 + - - +
1075G ILE* 5.3 1.1 - - + -
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Residues in contact with VAL1074 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028G ALA 3.6 0.9 - - - +
1029G ILE* 3.4 4.2 - - - -
1030G LYS* 2.7 40.2 + - + +
1044G PHE* 4.0 17.2 - - + -
1045G LEU* 5.6 0.2 - - + -
1048G ALA* 3.5 29.6 - - + -
1062G LEU* 3.7 19.3 - - + -
1064G GLY 3.7 10.1 - - - +
1065G VAL* 4.0 9.9 - - + -
1073G LEU* 1.3 79.0 - - - +
1075G ILE* 1.3 63.1 + - - +
1076G MET* 3.7 22.1 - - + +
1301G 66A 4.2 13.5 - - + -
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Residues in contact with ILE1075 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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991G VAL* 4.1 12.8 - - + -
996G ILE* 3.4 37.0 - - + -
1015G ALA* 4.2 7.6 - - + -
1018G VAL* 5.1 2.5 - - + -
1027G VAL* 3.5 42.8 - - + -
1028G ALA 3.4 2.7 - - - -
1029G ILE* 4.7 11.2 - - + -
1062G LEU* 3.5 5.2 - - - +
1063G LEU* 2.7 38.1 + - + -
1064G GLY* 2.9 28.5 + - - +
1066G VAL* 4.1 11.4 - - + -
1073G LEU* 5.3 0.4 - - + -
1074G VAL* 1.3 76.4 - - - +
1076G MET* 1.3 55.0 + - - +
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Residues in contact with MET1076 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010G VAL* 4.7 2.2 - - + -
1027G VAL* 3.7 5.7 - - - +
1028G ALA* 2.8 39.9 + - + +
1030G LYS* 3.7 31.0 - - + +
1051G MET* 4.3 10.8 - - + -
1060G VAL* 4.3 1.6 - - + -
1061G ARG 3.4 14.4 - - - +
1062G LEU* 4.4 1.3 - - + -
1063G LEU* 3.8 7.4 - - - +
1074G VAL* 3.7 15.9 - - + -
1075G ILE* 1.3 79.9 - - - +
1077G GLU* 1.3 72.0 + - - +
1078G LEU 3.1 0.7 + - - -
1301G 66A 3.5 66.9 - - + +
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Residues in contact with GLU1077 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026G ARG 5.5 0.2 - - - -
1059G VAL 4.0 2.3 - - - +
1060G VAL* 3.5 7.6 - - + +
1061G ARG* 3.0 49.9 + - + +
1063G LEU* 3.7 15.5 - - + +
1076G MET* 1.3 67.5 - - - +
1078G LEU* 1.3 65.5 + - - +
1079G MET* 3.5 18.1 + - - +
1147G LYS* 2.5 34.3 + - - -
1301G 66A 3.0 23.4 + - - -
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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