Contacts of the helix formed by residues 244 - 249 (chain S) in PDB entry 1G3I
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 ALA 244 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104S THR* 6.4 0.7 - - - -
107S ALA* 4.6 3.4 - - + +
108S MET* 3.1 40.2 - - + -
111S VAL* 4.1 22.4 - - + +
240S LEU 3.5 13.8 + - - +
241S LYS* 5.5 0.9 - - - -
243S LYS* 1.3 80.8 - - - +
245S ILE* 1.3 59.6 + - + +
247S ALA* 3.0 20.6 - - - +
248S VAL* 3.2 14.4 + - - +
295S HIS* 6.4 0.2 - - + -
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Residues in contact with ILE 245 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104S THR* 5.5 7.2 - - + +
108S MET* 6.0 0.2 - - + -
241S LYS 3.7 23.1 - - - +
242S GLN* 3.9 17.7 - - - +
243S LYS 4.0 1.2 - - - +
244S ALA* 1.3 76.0 - - + +
246S ASP* 1.3 57.9 + - - +
247S ALA 2.8 5.2 - - - -
248S VAL* 4.3 6.5 - - + +
249S GLU* 2.8 60.6 + - + +
293S THR* 4.9 1.3 - - - +
295S HIS* 3.9 26.9 - - + +
296S GLY* 4.0 13.7 - - - +
297S MET 3.9 19.3 - - - +
298S VAL* 4.4 11.9 - - + -
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Residues in contact with ASP 246 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242S GLN* 2.5 51.0 + - - +
243S LYS* 4.1 8.9 - - + +
244S ALA 3.4 0.4 - - - -
245S ILE* 1.3 76.0 - - - +
247S ALA* 1.3 61.0 + - - +
249S GLU* 4.0 11.8 - - - +
250S GLN* 3.8 17.7 + - - +
251S ASN* 5.0 1.0 + - - -
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Residues in contact with ALA 247 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77S PRO* 5.3 7.6 - - + -
107S ALA* 5.6 0.9 - - + -
111S VAL* 4.7 10.8 - - + -
243S LYS 3.9 9.2 + - - +
244S ALA* 3.0 17.8 + - - +
245S ILE 2.8 0.8 - - - -
246S ASP* 1.3 77.8 - - - +
248S VAL* 1.3 58.1 + - + +
250S GLN 3.1 1.4 + - - -
251S ASN* 2.4 53.9 + - + +
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Residues in contact with VAL 248 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77S PRO* 3.7 9.2 - - + +
100S ILE* 5.8 1.3 - - + -
103S LEU* 4.1 29.2 - - + +
104S THR* 4.1 17.9 - - + +
107S ALA* 3.7 29.6 - - + -
244S ALA 3.2 9.7 + - - +
245S ILE* 3.2 6.9 + - + +
247S ALA* 1.3 79.5 - - - +
249S GLU* 1.3 68.0 + - - +
250S GLN 2.7 4.0 + - - -
251S ASN 3.4 18.1 + - - -
252S GLY* 3.7 4.2 + - - -
298S VAL* 3.6 24.5 - - + -
299S LYS 5.2 0.2 - - - +
303S ILE* 4.7 8.3 - - + +
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Residues in contact with GLU 249 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242S GLN* 4.0 9.8 + - - -
245S ILE* 2.8 50.1 + - + +
246S ASP* 4.0 14.5 - - - +
248S VAL* 1.3 72.3 - - - +
250S GLN* 1.3 57.5 + - + +
297S MET 4.2 4.7 - - - +
298S VAL* 4.1 2.0 - - + -
299S LYS* 3.5 53.8 + - + +
302S HIS* 3.5 30.6 + - + +
303S ILE* 4.2 1.7 + - - +
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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