Contacts of the strand formed by residues 113 - 116 (chain G) in PDB entry 6NZD
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 GLN 113 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62G PRO 2.9 5.0 + - - +
63G ARG* 2.7 50.3 + - + +
64G ILE 2.9 23.6 + - - -
101G LYS* 3.4 25.1 - - - +
102G ASP 3.5 6.5 - - - +
103G ASP* 3.2 25.2 + - - +
112G PHE* 1.3 78.2 - - - +
114G ILE* 1.3 66.5 + - - +
115G TRP* 3.1 33.1 + - + +
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Residues in contact with ILE 114 (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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64G ILE* 3.5 35.9 - - + +
66G LEU* 3.9 29.2 - - + -
78G GLN* 4.0 14.6 - - + -
82G PHE* 3.6 38.4 - - + -
100G TYR 3.0 5.4 - - - +
101G LYS* 3.5 2.8 - - - -
102G ASP* 2.9 46.9 + - + +
104G ILE* 4.7 9.6 - - + -
110G VAL* 5.2 3.1 - - + -
113G GLN* 1.3 75.3 - - - +
115G TRP* 1.3 63.0 + - - +
116G ASP 4.6 1.3 - - - +
229G PHE* 4.1 4.9 - - + -
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Residues in contact with TRP 115 (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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63G ARG* 3.5 47.8 - - + -
64G ILE 2.9 13.2 + - - +
65G LEU* 3.5 16.4 - - + -
66G LEU 2.9 24.9 + - - +
99G ILE* 4.4 5.8 - - + -
100G TYR 3.4 1.6 - - - -
101G LYS* 3.4 44.5 - - + +
113G GLN* 3.1 24.7 + - + +
114G ILE* 1.3 76.9 - - - +
116G ASP* 1.3 62.5 + - - +
117G PHE* 3.5 19.4 + + + -
133G ILE* 3.4 48.0 - - + -
136G GLY* 5.5 1.3 - - - -
137G THR* 4.3 0.9 - - - -
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Residues in contact with ASP 116 (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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66G LEU* 3.7 14.6 - - + -
74G LYS* 3.4 28.4 - - - +
75G SER* 3.0 29.6 + - - -
78G GLN* 4.8 9.6 - - + +
96G THR* 3.6 14.0 + - - +
98G LYS 3.8 0.7 - - - +
99G ILE* 3.7 4.5 - - - -
100G TYR* 2.9 49.4 + - + +
114G ILE* 3.8 1.6 - - + -
115G TRP* 1.3 70.0 - - - +
117G PHE* 1.3 79.5 + - - +
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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