Contacts of the helix formed by residues 197 - 207 (chain A) in PDB entry 2W3C
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 ASN 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A PRO* 5.2 2.2 + - - +
158A GLN* 3.0 48.0 + - - +
159A GLN* 5.0 6.7 - - - +
162A LEU* 5.0 4.2 - - - +
193A LEU 4.2 4.0 - - - +
194A THR 3.0 7.4 + - - +
195A ARG 3.0 2.7 + - - +
196A SER* 1.3 76.0 + - - +
198A GLY* 1.3 63.3 + - - +
199A ALA* 3.9 7.1 + - - +
200A ILE* 3.1 31.4 + - + +
201A GLN* 3.2 28.0 + - - +
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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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196A SER 4.0 1.4 - - - -
197A ASN* 1.3 69.2 + - - +
199A ALA* 1.3 65.1 - - - +
201A GLN* 3.0 27.2 + - - +
202A LYS* 3.0 26.3 + - - +
243A ASN* 3.7 4.2 + - - -
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Residues in contact with ALA 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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162A LEU* 4.4 20.9 - - + -
197A ASN* 3.6 7.0 + - - +
198A GLY* 1.3 72.3 - - - +
200A ILE* 1.3 62.9 + - - +
202A LYS* 3.2 15.0 + - - +
203A ILE* 3.0 28.0 + - + +
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Residues in contact with ILE 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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158A GLN* 3.8 26.2 - - + +
162A LEU* 4.2 19.7 - - + +
168A VAL* 4.1 14.8 - - + -
193A LEU* 3.8 49.4 - - + +
194A THR* 4.3 4.3 - - + -
197A ASN* 3.1 32.1 + - + +
198A GLY 3.3 0.2 - - - -
199A ALA* 1.3 73.1 - - - +
201A GLN* 1.3 64.2 + - - +
203A ILE* 3.3 6.7 + - - +
204A VAL* 3.0 28.6 + - + +
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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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194A THR* 2.9 35.6 + - - +
196A SER* 4.0 7.1 - - - +
197A ASN 3.2 27.2 + - - +
198A GLY* 3.0 12.1 + - - +
200A ILE* 1.3 76.0 - - - +
202A LYS* 1.3 63.7 + - - +
204A VAL* 3.4 4.0 + - - +
205A ALA 3.2 16.5 + - - -
238A ASN* 3.1 31.8 + - - +
239A LEU* 3.7 12.2 - - - +
241A LYS 4.4 4.0 + - - +
242A ASN 5.4 0.7 - - - +
243A ASN* 2.7 36.1 + - - +
246A ASN* 3.3 13.9 + - - +
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Residues in contact with LYS 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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198A GLY* 3.0 28.2 + - - +
199A ALA* 3.4 10.7 - - - +
201A GLN* 1.3 76.3 - - - +
203A ILE* 1.3 57.4 + - + +
205A ALA* 3.2 4.9 + - - +
206A PHE* 3.0 49.9 + - + -
243A ASN* 3.8 14.5 - - - +
245A SER* 3.4 32.8 - - - +
246A ASN* 3.6 19.7 - - - +
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Residues in contact with ILE 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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162A LEU* 3.4 32.8 - - + -
168A VAL* 4.0 28.9 - - + -
169A SER* 5.2 3.4 - - - +
199A ALA* 3.0 17.0 + - + +
200A ILE* 3.3 9.8 + - - +
202A LYS* 1.3 72.0 - - + +
204A VAL* 1.3 60.5 + - - +
206A PHE* 3.1 18.6 + - + +
207A GLU* 2.9 39.4 + - + +
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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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168A VAL* 3.8 19.1 - - + -
172A MET* 3.8 18.7 - - - +
190A LEU* 4.8 8.5 - - + -
193A LEU* 4.9 0.7 - - + -
194A THR* 3.7 18.2 - - + -
200A ILE* 3.0 20.4 + - + +
201A GLN 3.6 5.6 - - - +
203A ILE* 1.3 75.3 - - - +
205A ALA* 1.3 57.4 + - - +
207A GLU* 3.2 19.7 + - - +
209A ALA* 3.1 40.1 + - + +
235A LEU* 5.3 6.3 - - + -
239A LEU* 3.7 17.7 - - + -
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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 3.2 1.4 + - - +
202A LYS 3.2 8.9 + - - +
203A ILE 3.2 0.6 - - - -
204A VAL* 1.3 74.8 - - - +
206A PHE* 1.3 66.6 + - + +
207A GLU 3.1 1.6 - - - -
208A ASN* 3.4 12.0 + - - -
209A ALA* 4.2 8.6 + - - +
210A PHE* 3.8 24.5 + - + -
239A LEU* 5.4 1.3 - - + -
246A ASN* 3.7 30.5 - - - +
249A PHE* 3.3 24.5 - - + -
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Residues in contact with PHE 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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202A LYS* 3.0 39.0 + - + -
203A ILE* 3.1 21.7 + - + +
205A ALA* 1.3 77.7 - - + +
207A GLU* 1.3 63.1 + - + +
208A ASN* 3.2 4.2 + - - +
245A SER* 5.6 4.9 - - - -
246A ASN* 5.0 5.8 - - - -
249A PHE* 4.7 25.4 - + + -
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Residues in contact with GLU 207 (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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168A VAL* 5.2 0.4 - - + -
169A SER* 3.3 41.7 + - - +
172A MET* 3.3 29.5 - - + +
203A ILE* 2.9 26.5 + - + +
204A VAL 3.5 5.8 - - - +
205A ALA 3.1 0.8 - - - -
206A PHE* 1.3 81.8 - - + +
208A ASN* 1.3 67.6 + - - +
209A ALA 3.3 2.7 - - - -
212A ARG* 3.4 7.6 + - - -
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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