Contacts of the helix formed by residues 242 - 250 (chain A) in PDB entry 3GNI
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 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A LEU 5.4 0.2 + - - -
196A LYS 4.5 0.7 - - - +
199A SER* 4.7 3.8 + - - -
200A ALA* 3.5 22.9 + - - +
203A LEU* 3.7 22.3 - - + +
236A LEU* 2.8 45.8 + - - +
237A LEU* 5.1 1.8 - - - -
239A ASP* 2.9 16.7 + - - +
241A HIS* 1.3 83.6 - - - +
243A PHE* 1.3 59.5 + - - +
244A THR 3.2 3.1 - - - -
245A ILE* 3.1 19.0 + - + -
246A MET* 2.8 28.0 + - - +
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Residues in contact with PHE 243 (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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237A LEU 5.5 0.7 - - - -
239A ASP 3.7 3.6 + - - -
240A ARG* 3.3 18.6 + - - +
241A HIS 3.5 1.8 + - - -
242A ASN* 1.3 77.3 - - - +
244A THR* 1.3 65.1 + - - +
246A MET* 3.4 30.5 - - + +
247A THR* 3.0 45.9 + - + -
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Residues in contact with THR 244 (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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204A GLU* 3.4 37.7 - - + +
241A HIS 5.2 0.8 + - - -
242A ASN 3.2 0.4 - - - -
243A PHE* 1.3 82.5 - - - +
245A ILE* 1.3 69.2 + - - +
247A THR* 2.9 19.9 + - - -
248A LYS* 3.2 13.9 + - + +
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Residues in contact with ILE 245 (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 ALA* 3.5 27.8 - - + +
203A LEU* 3.7 26.9 - - + +
204A GLU* 3.7 26.5 - - + +
207A TYR* 3.8 10.1 - - + -
211A PHE* 3.7 35.0 - - + -
237A LEU* 5.0 5.8 - - + -
241A HIS 4.9 1.1 - - - +
242A ASN* 3.1 25.7 + - + +
244A THR* 1.3 77.8 - - - +
246A MET* 1.3 64.3 + - - +
248A LYS* 3.3 7.4 + - - +
249A TYR* 3.0 21.2 + - + +
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Residues in contact with MET 246 (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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237A LEU* 3.6 46.9 - - + +
238A LEU* 6.1 1.6 - - - -
242A ASN 2.8 18.8 + - - +
243A PHE* 3.4 28.5 - - + +
245A ILE* 1.3 74.7 - - - +
247A THR* 1.3 92.4 + - + +
249A TYR* 3.2 1.2 + - - +
250A ILE* 3.1 37.6 + - + +
280A VAL* 3.6 31.9 - - + -
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Residues in contact with THR 247 (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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243A PHE* 3.0 32.6 + - + +
244A THR* 2.9 20.3 + - - -
246A MET* 1.3 99.7 - - + +
248A LYS* 1.3 64.7 + - - +
250A ILE* 3.8 11.0 - - + +
251A SER* 3.6 19.2 + - - -
284A ASN* 5.6 3.4 - - - +
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Residues in contact with LYS 248 (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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204A GLU* 4.1 19.9 + - - +
207A TYR* 3.8 45.2 - - + +
208A ASP* 5.0 8.3 + - - -
244A THR* 3.2 13.2 + - + +
245A ILE* 3.4 10.3 - - - +
247A THR* 1.3 79.5 + - - +
249A TYR* 1.3 61.8 + - - +
251A SER* 2.6 25.0 + - - +
252A LYS* 3.7 21.7 - - - +
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Residues in contact with TYR 249 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A TYR* 3.1 21.1 + - + +
211A PHE* 4.0 32.5 - + + -
218A LEU* 4.2 6.3 - - + +
233A LEU* 3.4 22.8 - - + +
237A LEU* 3.8 34.1 - - + -
245A ILE* 3.0 14.8 + - + +
246A MET 3.2 4.7 + - - +
248A LYS* 1.3 77.5 - - - +
250A ILE* 1.3 60.0 + - + +
251A SER 3.2 3.9 + - - -
252A LYS 3.5 4.2 + - - -
255A ASN* 2.8 56.5 + - + +
258A LEU* 4.6 1.7 - - - +
259A MET* 3.5 13.8 - - + +
277A VAL* 4.3 4.0 - - + -
281A PHE* 3.7 27.1 - + - -
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Residues in contact with ILE 250 (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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237A LEU* 4.9 3.6 - - + -
246A MET* 3.2 29.2 - - + +
247A THR* 3.8 15.0 - - + +
249A TYR* 1.3 81.2 - - + +
251A SER* 1.3 58.6 + - - +
252A LYS 3.5 0.9 - - - -
280A VAL* 3.9 30.1 - - + +
281A PHE* 3.5 49.3 - - + +
284A ASN* 3.6 46.9 + - + +
291A ILE* 3.7 11.1 - - - +
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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