Contacts of the helix formed by residues 189 - 194 (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 GLU 189 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G GLN* 4.0 11.3 - - - +
125G GLY* 3.3 34.9 - - - +
126G ASN* 4.7 3.8 - - + -
186G THR* 3.0 27.9 + - + +
187G LEU 3.0 2.0 + - - -
188G GLU* 1.3 77.2 - - + +
190G PRO* 1.3 58.7 - - - +
191G ILE* 3.1 8.5 - - + +
192G ASN* 2.6 38.9 + - - +
193G HIS* 3.3 8.1 + - - -
221G TYR* 2.7 37.5 + - - -
2128G FBP 4.0 9.4 + - - +
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Residues in contact with PRO 190 (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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125G GLY 3.4 13.9 - - - +
126G ASN* 3.3 31.6 - - + +
127G VAL 4.5 2.7 - - - +
148G ILE* 4.0 30.0 - - + +
149G GLU* 6.2 0.9 - - - -
188G GLU 3.6 3.1 - - - +
189G GLU* 1.3 82.2 - - - +
191G ILE* 1.3 62.6 + - + +
193G HIS* 3.2 19.3 - - + -
194G ALA* 3.0 30.3 + - + +
195G LYS 3.5 1.6 + - - -
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Residues in contact with ILE 191 (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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125G GLY* 4.0 20.2 - - - +
146G ALA 5.7 4.5 - - - +
147G SER* 6.0 1.3 - - - -
148G ILE* 3.8 21.9 - - + +
161G TYR* 3.2 38.6 - - + -
189G GLU* 2.8 17.9 + - + +
190G PRO* 1.3 77.8 - - - +
192G ASN* 1.3 67.2 + - - +
195G LYS* 3.1 21.0 - - - +
196G LYS* 3.3 36.4 + - + +
2128G FBP 6.2 0.2 - - - +
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Residues in contact with ASN 192 (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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184G SER* 4.3 9.1 - - - +
185G GLY 3.4 31.9 + - - +
186G THR 3.5 8.7 + - - +
187G LEU* 4.7 2.5 - - - -
189G GLU* 2.6 21.2 + - - +
191G ILE* 1.3 75.2 - - - +
193G HIS* 1.3 66.8 + - - +
194G ALA 3.2 0.9 - - - -
195G LYS 3.2 0.3 + - - -
196G LYS* 3.0 44.5 + - - +
197G VAL* 3.1 13.0 + - + -
221G TYR* 2.9 33.2 + - - -
246G GLY* 5.6 1.9 - - - +
2128G FBP 5.1 0.4 + - - -
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Residues in contact with HIS 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187G LEU* 2.9 33.2 + - + +
188G GLU* 4.2 7.4 - - - -
189G GLU 3.3 12.1 + - - -
190G PRO* 3.2 31.2 - - + -
192G ASN* 1.3 80.0 - - - +
194G ALA* 1.3 69.0 + - + +
197G VAL* 3.3 27.1 - - + +
198G LYS* 3.7 7.4 - - - +
966G SO4 3.2 52.9 + - - +
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Residues in contact with ALA 194 (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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148G ILE* 5.7 0.9 - - + -
162G GLU* 5.3 1.0 - - - +
190G PRO* 3.0 21.4 + - + +
193G HIS* 1.3 96.1 - - + +
195G LYS* 1.3 73.4 + - + +
198G LYS* 3.2 17.9 - - - +
966G SO4 3.7 12.3 - - - +
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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