Contacts of the strand formed by residues 201 - 206 (chain A) in PDB entry 4NDH
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 HIS 201 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LYS* 3.9 4.7 - - - +
193A ASP* 3.0 44.1 + - + +
196A PRO* 3.6 23.8 - - + +
197A LYS* 3.0 28.4 + - + +
198A ALA 4.4 2.4 + - - +
199A ARG 4.2 0.4 - - - -
200A TYR* 1.3 76.3 - - - +
202A TRP* 1.3 77.2 + - - +
262A HIS* 2.9 23.7 + - - -
263A VAL 3.4 7.4 - - - -
264A ILE* 3.7 17.8 - - + +
282A PHE* 3.7 20.5 - + - -
401A AMP 3.5 10.5 - - - -
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Residues in contact with TRP 202 (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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182A VAL* 4.0 27.0 - - + +
190A VAL* 3.8 13.7 - - + -
191A ILE 3.2 15.7 - - - +
192A LYS* 4.0 18.4 - - + +
193A ASP 4.1 0.4 - - - +
200A TYR* 3.7 34.1 - + + -
201A HIS* 1.3 79.5 - - - +
203A LEU* 1.3 70.5 + - - +
234A VAL* 3.6 25.6 - - + -
235A ILE* 4.3 5.4 - - + -
238A PHE* 3.7 30.5 - + + -
239A ALA* 4.4 4.0 - - + -
246A PHE* 3.7 26.0 - + - -
262A HIS* 3.7 0.2 - - - -
263A VAL* 2.9 58.4 + - + +
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Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 3.9 26.7 - - + -
190A VAL* 3.3 4.1 - - - +
191A ILE* 2.9 40.4 + - + -
193A ASP* 3.6 21.8 - - + +
201A HIS* 4.2 0.4 - - - +
202A TRP* 1.3 80.4 - - - +
204A VAL* 1.3 62.2 + - - +
205A LEU* 3.6 14.8 - - + +
260A HIS* 4.2 11.9 - - + -
261A LEU 3.2 4.7 - - - +
262A HIS* 3.5 37.2 - - + +
401A AMP 3.7 28.7 - - - +
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Residues in contact with VAL 204 (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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188A VAL* 4.1 13.7 - - + -
189A VAL 3.5 7.9 - - - +
190A VAL* 4.1 22.0 - - + +
203A LEU* 1.3 75.9 - - - +
205A LEU* 1.3 62.0 + - - +
227A MET* 3.5 46.5 - - + +
230A VAL* 4.4 2.0 - - + -
231A GLY* 4.2 7.2 - - - +
260A HIS* 3.3 4.2 - - - -
261A LEU* 2.8 40.8 + - + +
263A VAL* 3.8 26.5 - - + -
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Residues in contact with LEU 205 (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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171A LEU* 4.0 27.8 - - + -
175A MET* 4.3 11.9 - - + -
188A VAL* 3.3 5.4 - - - -
189A VAL* 2.8 54.2 + - + +
191A ILE* 3.9 23.6 - - + -
203A LEU* 3.6 22.7 - - + +
204A VAL* 1.3 77.6 - - - +
206A PRO* 1.3 71.2 - - + +
258A HIS* 3.8 23.6 - - + +
259A VAL 3.9 1.1 - - - +
260A HIS* 3.8 20.0 - - + -
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Residues in contact with PRO 206 (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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175A MET* 3.3 4.7 - - - +
187A GLN 3.4 7.9 - - - +
188A VAL* 4.0 3.8 - - + -
205A LEU* 1.3 85.5 - - + +
207A TRP* 1.3 60.4 + - - +
208A THR* 3.7 17.5 - - + +
210A ILE* 4.5 9.9 - - + -
223A LEU* 3.7 37.9 - - + -
227A MET* 3.9 18.2 - - + -
258A HIS* 2.7 33.2 + - + +
259A VAL* 3.3 22.9 - - + +
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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