Contacts of the helix formed by residues 201 - 207 (chain A) in PDB entry 4ILG
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 LYS 201 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A PHE* 3.6 46.2 + - + +
189A ILE* 6.1 0.2 - - - +
197A ASP 3.8 11.0 + - - +
198A PHE* 2.9 53.3 + - - +
200A ASP* 1.3 69.6 - - - +
202A SER* 1.3 50.9 + - - +
203A TYR 3.3 2.9 - - - -
204A TYR* 3.0 14.3 + - + +
205A LEU 2.8 31.4 + - - -
248A GLU* 4.0 16.8 - - - -
249A LEU* 4.1 14.4 - - + +
252A SER* 2.9 30.6 + - - +
253A SER* 3.1 13.6 + - - +
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Residues in contact with SER 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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200A ASP* 2.7 29.2 + - - -
201A LYS* 1.3 74.0 - - - +
203A TYR* 1.3 61.7 + - - +
206A ASN* 2.8 39.4 + - - +
253A SER* 3.3 9.6 + - - -
254A ALA 3.0 2.4 + - - -
255A THR* 2.9 41.9 + - - -
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Residues in contact with TYR 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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187A GLU 5.3 4.0 - - - -
188A ALA 5.5 3.1 - - - +
190A ARG* 3.7 60.6 - - + +
197A ASP* 4.4 13.2 - - - +
200A ASP 4.6 1.8 + - - +
201A LYS 3.3 0.6 - - - -
202A SER* 1.3 78.6 - - - +
204A TYR* 1.3 64.0 + - - +
206A ASN* 5.2 0.4 - - - -
207A THR* 3.1 55.3 + - + +
208A VAL* 3.3 28.4 + - + -
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Residues in contact with TYR 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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180A VAL 3.8 2.3 + - - -
181A ILE* 3.3 18.2 - - + -
182A ASN 3.0 29.5 + - - -
183A PHE* 4.0 20.2 - + - -
185A SER* 4.3 2.6 + - - -
187A GLU* 3.8 7.2 - - + +
188A ALA* 3.6 51.9 + - + +
197A ASP 5.9 0.2 - - - +
201A LYS* 3.0 16.4 + - + +
203A TYR* 1.3 81.6 - - - +
205A LEU* 1.3 65.0 + - - +
208A VAL* 3.4 24.5 - - + +
209A MET* 3.0 50.9 + - + +
249A LEU* 3.7 16.8 - - + -
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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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201A LYS 2.8 10.4 + - - +
202A SER 4.0 2.7 - - - +
204A TYR* 1.3 75.4 - - - +
206A ASN* 1.3 60.0 + - - +
209A MET* 3.4 4.3 - - + +
210A LEU* 2.8 53.7 + - + +
220A TYR* 4.3 12.1 - - + -
249A LEU* 3.7 34.7 - - + +
250A ILE* 4.1 13.0 - - + -
253A SER* 3.5 24.2 - - - +
255A THR 4.0 6.3 - - - +
256A VAL* 3.7 38.4 - - + -
260A MET* 5.0 1.8 - - - -
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Residues in contact with ASN 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 SER* 2.8 35.7 + - - +
203A TYR* 5.2 0.2 - - - -
205A LEU* 1.3 77.1 - - - +
207A THR* 1.3 62.1 + - - +
210A LEU* 3.6 8.0 - - - +
211A GLN* 2.9 49.8 + - - +
255A THR* 2.9 35.6 + - - +
257A PRO* 3.5 28.2 - - - +
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Residues in contact with THR 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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203A TYR* 3.1 54.0 + - + +
206A ASN* 1.3 78.1 - - - +
208A VAL* 1.3 65.7 + - + +
211A GLN* 3.7 17.0 + - + +
212A GLY* 3.2 18.9 + - - -
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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