Contacts of the strand formed by residues 76 - 79 (chain G) in PDB entry 5DPW
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 TYR 76 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C TYR* 4.7 18.6 - + + -
77C LEU 5.7 0.9 + - - -
84C LEU* 3.5 45.3 - - + +
85C VAL 2.4 24.8 + - - -
87C MET* 3.4 42.8 - - + +
60G LEU* 5.0 1.6 - - - -
74G ALA 5.3 0.7 - - - -
75G PHE* 1.3 81.3 - - - +
77G LEU* 1.3 63.4 + - - +
78G LEU* 4.0 7.5 - - + +
84G LEU* 4.6 6.5 - - + -
108G THR 3.7 0.5 - - - +
109G TYR* 3.1 7.1 - - - +
110G ALA* 2.8 43.7 + - + +
111G SER 3.3 22.7 - - - -
112G GLN* 4.6 1.1 - - - -
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Residues in contact with LEU 77 (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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76C TYR* 5.4 2.3 + - - -
31G VAL* 5.2 1.6 - - + -
56G MET* 3.7 38.9 - - + +
59G PHE* 4.3 2.2 - - + -
60G LEU* 3.7 42.3 - - + +
63G ILE* 3.7 30.7 - - + -
75G PHE* 4.4 4.9 - - + -
76G TYR* 1.3 73.6 - - - +
78G LEU* 1.3 60.9 + - - +
79G VAL* 4.0 1.9 + - - +
83G SER 4.1 2.4 - - - +
84G LEU* 3.7 17.3 - - - +
85G VAL* 5.2 2.1 + - - +
87G MET* 5.9 2.7 - - + +
107G MET* 4.1 15.0 - - + -
108G THR 3.3 5.4 - - - +
109G TYR* 3.9 22.2 - - + -
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Residues in contact with LEU 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU* 4.4 10.1 - - + -
76G TYR* 4.0 11.9 - - + +
77G LEU* 1.3 74.5 - - - +
79G VAL* 1.3 60.7 + - - +
81G ASN* 3.0 26.5 + - - +
82G LYS 4.1 4.3 - - - +
83G SER 3.5 6.3 - - - +
84G LEU* 4.4 12.3 - - + -
107G MET* 4.3 0.7 - - - -
108G THR* 2.8 46.2 + - + +
110G ALA* 4.0 21.3 - - + -
113G GLU* 3.8 20.9 - - + +
115G PHE* 3.3 41.3 - - + -
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Residues in contact with VAL 79 (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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56G MET* 4.3 13.2 - - + -
77G LEU 4.0 0.8 - - - +
78G LEU* 1.3 66.3 - - - +
80G ASN* 1.3 72.6 + - - +
81G ASN 3.0 3.6 - - - -
83G SER* 3.0 41.5 + - - +
85G VAL* 4.0 15.3 - - + -
94G ILE* 4.0 20.4 - - + -
98G TYR* 3.6 34.3 - - + +
105G VAL* 5.0 2.2 - - + -
106G TYR 3.3 14.6 - - - +
107G MET* 3.8 19.3 - - + +
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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