Contacts of the helix formed by residues 196 - 205 (chain A) in PDB entry 1N4V
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 ASP 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A ASN* 3.8 9.2 - - - +
194A VAL 3.5 2.9 + - - +
195A TYR* 1.3 77.2 - - - +
197A PHE* 1.3 58.8 + - - +
198A GLY* 2.9 19.1 + - - -
199A TYR* 3.0 24.0 + - + +
200A MET 3.0 21.7 + - - -
202A ARG* 4.4 7.7 + - - -
224A GLY* 2.9 18.7 + - - +
226A GLN* 4.9 9.8 + - + +
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Residues in contact with PHE 197 (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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158A ASN* 3.0 31.6 + - - +
159A HIS* 3.5 8.5 - - - +
160A ILE* 3.3 65.1 - - + -
161A ASP 5.0 1.6 - - - +
164A TRP* 5.3 2.7 - + + -
171A TYR* 4.1 5.6 - - - -
191A VAL 4.4 10.3 - - - -
193A ASN* 3.5 35.9 - - + -
195A TYR 3.1 6.7 + - - -
196A ASP* 1.3 69.4 - - - +
198A GLY* 1.3 60.2 + - - +
200A MET* 3.3 34.7 + - + +
201A GLN* 3.0 32.2 + - - +
343A ILE* 4.6 5.4 - - + -
344A PRO 4.8 4.5 - - - -
345A ALA* 4.9 3.1 - - + -
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Residues in contact with GLY 198 (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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158A ASN* 4.4 1.4 + - - -
196A ASP* 2.9 8.8 + - - -
197A PHE* 1.3 75.9 - - - +
199A TYR* 1.3 63.8 + - - +
201A GLN* 3.2 13.6 + - - +
202A ARG* 3.2 36.1 + - - +
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Residues in contact with TYR 199 (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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195A TYR* 4.2 0.7 - - - -
196A ASP* 3.0 31.2 + - + +
198A GLY* 1.3 75.5 - - - +
200A MET* 1.3 58.6 + - - +
202A ARG* 3.0 28.8 + - - +
203A GLU* 2.9 46.8 + - + -
208A VAL* 3.4 22.2 - - + +
209A PRO* 2.7 42.9 + - - +
223A HIS* 3.3 32.1 + - + +
224A GLY* 4.0 16.6 - - - -
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Residues in contact with MET 200 (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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164A TRP* 3.8 16.3 - - + -
171A TYR* 3.4 38.6 - - - +
195A TYR* 3.7 24.5 - - + -
196A ASP 3.0 11.5 + - - +
197A PHE* 3.5 29.2 - - + +
198A GLY 3.2 0.2 - - - -
199A TYR* 1.3 77.6 - - - +
201A GLN* 1.3 62.7 + - - +
203A GLU* 3.2 22.4 + - - +
204A ALA* 3.1 18.0 + - - +
212A ALA* 4.1 2.0 - - + -
213A LEU* 3.8 17.2 - - + +
341A SER* 3.6 14.6 - - - +
343A ILE* 3.9 11.0 - - + -
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Residues in contact with GLN 201 (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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161A ASP* 3.4 29.7 + - - +
164A TRP* 3.7 49.4 + - + +
197A PHE* 3.0 20.5 + - - +
198A GLY* 3.2 11.7 + - - +
200A MET* 1.3 75.3 - - - +
202A ARG* 1.3 64.4 + - + +
204A ALA* 3.2 5.0 + - - +
205A ALA* 3.1 21.7 + - - +
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Residues in contact with ARG 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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196A ASP* 4.4 8.3 + - - -
198A GLY* 3.2 18.9 + - - +
199A TYR* 3.0 41.1 + - - +
201A GLN* 1.3 77.6 - - + +
203A GLU* 1.3 63.1 + - - +
205A ALA* 3.3 3.7 + - - -
206A GLY 3.2 3.8 + - - -
207A GLU* 2.9 53.1 + - + +
208A VAL* 3.7 27.1 - - + +
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Residues in contact with GLU 203 (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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195A TYR* 2.6 26.2 + - - -
199A TYR* 2.9 39.5 + - + +
200A MET* 3.3 19.8 - - - +
202A ARG* 1.3 76.4 - - - +
204A ALA* 1.3 62.7 + - - +
206A GLY* 3.0 11.3 + - - -
208A VAL* 3.5 10.7 - - + +
209A PRO 3.8 7.6 - - - +
210A LYS* 3.2 27.9 + - + +
211A SER 2.8 26.7 + - - -
212A ALA 3.3 0.2 + - - -
213A LEU* 3.0 29.9 + - + +
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Residues in contact with ALA 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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164A TRP* 3.9 24.0 - - + +
168A THR* 4.7 1.1 - - - +
170A TRP* 3.9 17.8 + - + +
200A MET 3.1 2.8 + - - -
201A GLN 3.2 8.0 + - - +
203A GLU* 1.3 81.3 - - - +
205A ALA* 1.3 59.7 - - - +
206A GLY 3.2 0.9 + - - -
210A LYS* 4.9 3.6 + - - +
213A LEU* 3.6 20.4 - - + -
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Residues in contact with ALA 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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201A GLN 3.1 15.5 + - - +
202A ARG* 3.8 1.6 - - - +
203A GLU 3.2 0.4 - - - -
204A ALA* 1.3 76.9 - - - +
206A GLY* 1.3 60.0 + - - +
207A GLU* 3.5 30.4 + - + +
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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