Contacts of the strand formed by residues 183 - 191 (chain A) in PDB entry 3NZI
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 VAL 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A ILE* 3.6 19.1 - - + +
180A ALA 3.3 12.3 + - - +
181A PRO 3.2 2.9 - - - +
182A ALA* 1.3 80.9 - - - +
184A VAL* 1.3 71.7 + - - +
205A SER* 5.6 0.2 - - - -
206A GLY 3.5 9.0 - - - +
207A PHE* 4.8 0.2 - - + -
233A LYS* 4.2 12.8 + - - -
265A LEU* 4.7 5.8 - - + -
282A ILE* 3.6 51.8 - - + +
283A GLY* 4.8 4.3 - - - +
290A ASN* 3.9 11.0 - - - +
331A PRO* 3.8 24.9 - - + -
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Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PRO 5.1 0.7 - - - +
182A ALA 4.4 0.2 - - - +
183A VAL* 1.3 82.4 - - - +
185A HIS* 1.3 58.7 + - - +
186A ILE* 4.6 7.0 - - + -
205A SER* 3.5 6.8 + - - -
206A GLY* 2.6 62.6 + - - +
207A PHE* 4.1 0.4 - - - +
208A ILE* 3.8 24.0 - - + -
215A ILE* 3.9 18.8 - - + -
230A VAL* 3.9 14.8 - - + -
231A GLU 3.6 8.3 - - - +
232A LEU* 3.6 29.4 - - + -
284A SER* 5.0 0.6 + - - -
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Residues in contact with HIS 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A VAL* 1.3 71.0 - - - +
186A ILE* 1.3 73.1 + - - +
187A GLU* 3.8 23.2 + - + +
203A SER* 2.9 22.7 + - - -
204A GLY 3.4 15.0 - - - -
230A VAL* 3.6 3.1 - - - -
231A GLU* 2.8 64.6 + - + +
284A SER* 3.6 20.9 - - - +
287A SER* 4.3 16.1 - - - -
289A GLN* 3.8 26.3 - - + +
290A ASN 5.5 0.4 - - - +
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Residues in contact with ILE 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A VAL* 4.6 8.1 - - + -
185A HIS* 1.3 80.7 - - - +
187A GLU* 1.3 69.4 + - - +
188A LEU* 4.1 15.9 - - + +
203A SER* 3.6 2.6 - - - -
204A GLY 2.9 35.7 + - - +
205A SER 3.3 20.0 - - - +
206A GLY* 4.0 3.8 - - - +
215A ILE* 5.0 5.6 - - + -
217A THR* 3.1 40.6 - - + +
221A VAL* 4.2 10.8 - - + -
222A VAL* 4.4 9.4 - - + -
228A VAL* 4.6 4.5 - - + -
229A LYS 3.7 11.7 - - - +
230A VAL* 4.6 10.3 - - + -
254A ILE* 5.5 4.9 - - + -
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Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A HIS* 3.8 25.1 - - + +
186A ILE* 1.3 77.7 - - - +
188A LEU* 1.3 70.4 + - - +
189A PHE* 4.0 28.4 - - + -
200A PRO* 5.4 5.8 - - + +
202A ALA 4.2 3.6 - - - +
203A SER* 4.9 0.7 - - - +
228A VAL* 3.6 0.9 - - - -
229A LYS* 3.2 39.6 + - + +
231A GLU* 3.6 27.1 - - + +
237A THR* 4.7 10.6 + - - +
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Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ILE* 4.1 11.4 - - + +
187A GLU* 1.3 85.2 - - - +
189A PHE* 1.3 59.7 + - - +
200A PRO* 3.1 8.2 - - - +
201A VAL* 2.7 36.1 + - + -
202A ALA* 3.1 43.0 + - + +
203A SER 4.9 0.4 - - - +
220A HIS 5.4 1.1 - - - +
221A VAL* 2.5 33.0 - - + +
222A VAL* 4.3 3.4 - - + +
225A LYS* 4.2 18.4 - - + -
227A ARG 3.8 3.4 - - - +
228A VAL* 3.9 26.5 - - + -
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Residues in contact with PHE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLU* 4.0 28.9 - - + -
188A LEU* 1.3 78.7 - - - +
190A ARG* 1.3 61.1 + - - +
198A GLU* 3.9 33.7 - - + +
199A VAL 3.4 7.9 - - - +
200A PRO* 3.3 46.2 - - + -
201A VAL* 4.2 1.3 - - - -
225A LYS* 4.1 2.7 - - - +
226A HIS* 3.2 25.4 + - - +
227A ARG* 3.3 22.3 + - + +
229A LYS* 3.7 45.3 - - + -
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Residues in contact with ARG 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A PHE* 1.3 76.1 - - - +
191A LYS* 1.3 67.0 + - - +
198A GLU* 3.4 5.1 - - - -
199A VAL* 3.0 32.3 + - - +
201A VAL* 3.9 22.6 - - + +
224A ASN 5.1 5.4 + - - -
225A LYS* 4.8 8.3 - - + +
226A HIS* 3.8 32.5 + - - +
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Residues in contact with LYS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ARG* 1.3 84.3 + - - +
192A LEU* 1.3 71.2 + - - +
193A PRO* 4.6 0.3 - - - +
195A SER 4.0 19.3 + - - +
196A LYS* 4.4 8.0 - - - +
197A ARG 3.2 13.9 - - - +
198A GLU* 4.0 15.7 - - + +
226A HIS* 3.6 41.9 + - + +
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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