Contacts of the strand formed by residues 62 - 67 (chain G) in PDB entry 2NZV
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 THR 62 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G THR* 3.0 26.4 + - - +
61G THR* 1.3 81.5 - - - +
63G VAL* 1.3 60.4 + - - +
91G TYR* 4.4 1.1 - - - -
92G ASN* 3.0 38.8 - - + +
94G ILE* 4.2 21.2 - - + +
115G LYS 5.3 0.5 + - - -
116G GLN 4.0 3.6 + - - -
117G VAL* 3.2 29.9 - - - +
118G ASP* 3.5 4.5 + - - -
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Residues in contact with VAL 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G THR* 1.3 74.2 - - - +
64G GLY* 1.3 61.9 + - - +
65G VAL* 5.0 0.4 - - + -
91G TYR* 3.6 26.7 - - + -
92G ASN 2.7 10.9 + - - +
93G ILE* 3.1 31.9 - - + +
94G ILE* 3.2 3.6 + - - -
117G VAL* 4.5 0.9 - - - -
118G ASP 4.3 0.4 - - - -
119G GLY* 3.3 38.1 - - - +
302G MET* 4.1 20.9 - - + -
305G LEU* 3.4 11.4 - - + -
309G MET* 3.4 20.6 - - + -
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Residues in contact with GLY 64 (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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62G THR 3.9 1.2 + - - -
63G VAL* 1.3 74.3 - - - +
65G VAL* 1.3 57.9 + - - +
94G ILE* 3.8 7.2 - - - -
112G MET* 3.6 26.5 - - - -
117G VAL* 4.1 5.7 - - - +
119G GLY 2.9 12.7 + - - -
120G ILE* 3.1 6.3 - - - -
121G ILE* 2.8 31.2 + - - +
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Residues in contact with VAL 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G VAL 4.6 1.1 - - - +
64G GLY* 1.3 79.5 - - - +
66G ILE* 1.3 63.9 + - - +
67G ILE* 5.4 0.7 - - + -
79G ALA* 6.5 0.9 - - + -
82G ILE* 4.2 22.9 - - + -
93G ILE* 4.4 19.5 - - + -
94G ILE 3.3 7.4 + - - +
95G LEU* 3.2 39.9 - - + +
96G SER 3.2 17.2 + - - -
112G MET* 3.7 2.2 - - - +
121G ILE* 3.6 25.1 - - + -
123G MET* 6.3 2.0 - - - -
302G MET* 5.2 1.1 - - + -
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Residues in contact with ILE 66 (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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65G VAL* 1.3 73.4 - - - +
67G ILE* 1.3 61.1 + - - +
96G SER 3.5 4.3 - - - +
98G SER* 4.2 11.7 - - - +
105G GLU* 4.1 8.5 - - + +
108G LEU* 3.7 29.8 - - + +
109G LEU* 3.6 40.4 - - + +
112G MET* 3.4 26.2 - - + -
120G ILE* 4.9 5.8 - - + -
121G ILE 3.2 11.3 + - - +
122G PHE* 3.9 23.6 - - + -
123G MET* 3.1 31.4 + - - +
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Residues in contact with ILE 67 (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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65G VAL* 4.0 2.1 - - + -
66G ILE* 1.3 74.0 - - - +
68G PRO* 1.3 74.6 - - + +
69G ASP 4.1 1.3 - - - +
70G ILE* 3.5 17.3 - - + -
75G TYR* 3.2 50.0 - - + +
79G ALA* 4.5 6.3 - - + -
95G LEU* 3.4 24.0 - - + -
96G SER 3.0 6.5 + - - +
97G ASN* 3.0 30.3 - - - +
98G SER* 2.9 23.7 + - - -
123G MET* 3.8 17.3 - - + -
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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