Contacts of the helix formed by residues 173 - 179 (chain E) in PDB entry 1NZB
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 ARG 173 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172E LEU* 1.3 76.9 - - - +
174E ILE* 1.3 65.7 + - - +
175E ALA* 5.4 0.4 - - + -
176E GLU* 2.8 48.9 + - + +
177E ILE* 3.3 7.8 + - - +
288E GLY 6.1 0.4 - - - -
289E HIS* 2.9 33.5 + - - -
292E ARG* 3.0 26.2 - - - +
124G A 5.4 12.6 - - - -
125G T 3.9 19.1 + - - +
115H G 3.6 2.4 + - - -
116H C 2.7 54.1 + - - -
117H A 5.4 4.5 + - - -
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Residues in contact with ILE 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E PHE* 5.0 3.6 - - + -
172E LEU 5.5 0.7 - - - +
173E ARG* 1.3 69.2 - - - +
175E ALA* 1.3 70.6 + - - +
176E GLU 2.9 1.8 - - - -
177E ILE* 2.7 32.5 + - - +
178E ALA* 3.1 9.4 + - - -
258E THR* 3.6 29.6 - - - +
261E LEU* 3.9 21.1 - - + +
262E GLU* 3.9 24.0 - - + +
265E PHE* 4.8 8.7 - - + -
288E GLY* 3.4 34.7 + - - +
125G T 3.6 34.6 + - + +
126G A 4.7 0.2 - - - +
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Residues in contact with ALA 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E ARG* 5.4 0.7 - - + -
174E ILE* 1.3 85.5 - - + +
176E GLU* 1.3 59.3 + - - +
178E ALA* 3.5 9.0 + - - +
179E ARG* 3.0 46.6 + - - +
258E THR* 4.6 12.1 - - + -
124G A 5.3 2.2 - - - -
125G T 3.3 26.7 + - - +
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Residues in contact with GLU 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E LEU 4.9 0.2 - - - +
172E LEU* 2.8 31.9 - - + +
173E ARG* 2.8 57.6 + - + +
174E ILE 2.8 0.6 + - - -
175E ALA* 1.3 78.4 - - + +
177E ILE* 1.3 60.7 + - - +
179E ARG* 3.6 18.7 + - - +
180E ILE* 3.2 22.9 + - - +
197E ILE* 4.3 15.4 - - + +
200E THR* 5.0 10.6 - - + +
211E LYS* 5.8 0.2 + - - -
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Residues in contact with ILE 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E PHE* 4.3 18.8 - - + -
166E ILE* 3.3 29.6 - - + -
167E ALA* 4.8 7.9 - - + +
172E LEU* 3.6 31.4 - - + +
173E ARG 3.4 13.2 - - - +
174E ILE* 2.7 17.5 + - - +
176E GLU* 1.3 68.6 - - - +
178E ALA* 1.3 65.4 + - - +
179E ARG 2.9 3.8 + - - -
180E ILE* 2.9 31.3 + - + +
239E PHE* 3.7 34.6 + - + +
261E LEU* 4.3 6.7 - - + -
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Residues in contact with ALA 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E ILE 3.1 5.0 + - - +
175E ALA* 3.6 13.5 - - - +
177E ILE* 1.3 79.3 - - - +
179E ARG* 1.3 56.3 + - - +
180E ILE 3.7 3.3 + - - +
237E TYR* 4.0 7.6 - - - +
239E PHE* 5.0 6.1 - - - +
255E GLN* 2.8 38.6 - - + +
256E LEU* 3.9 22.8 + - - +
257E SER 5.3 0.2 - - - -
258E THR* 5.1 8.3 - - + +
261E LEU* 3.8 14.9 - - + +
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Residues in contact with ARG 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E ALA* 3.0 44.5 + - - +
176E GLU* 3.6 18.2 + - - +
177E ILE 2.9 1.2 + - - -
178E ALA* 1.3 76.9 - - - +
180E ILE* 1.3 64.4 - - - +
181E ARG* 3.6 16.1 + - - +
184E ASP* 5.0 0.7 - - - +
198E GLY 5.6 1.8 + - - -
199E ARG* 3.8 39.2 + - - +
200E THR* 5.6 2.0 - - - +
201E LYS* 4.6 26.8 - - - +
237E TYR* 4.5 7.1 - - + +
255E GLN* 3.0 33.7 + - - +
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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