Contacts of the strand formed by residues 239 - 242 (chain D) in PDB entry 4QGC
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 MET 239 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71D VAL* 4.1 11.4 - - + -
109D ALA* 3.8 26.9 - - + -
110D VAL 3.5 1.8 + - - +
111D ALA* 3.5 18.8 - - + -
112D LEU* 2.9 24.9 + - - +
237D VAL* 3.5 3.1 - - - +
238D ASP* 1.3 88.8 - - + +
240D VAL* 1.3 66.1 + - - +
241D PHE* 3.7 27.6 - - + -
265D ILE* 3.8 3.1 - - - +
266D LYS* 3.2 20.2 - - + +
268D ILE* 4.8 1.6 - - + -
461D ARG 4.6 0.7 - - - +
462D GLN* 4.4 11.9 - - + -
464D HIS* 6.1 0.2 - - + -
465D LEU* 3.7 40.2 - - + -
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Residues in contact with VAL 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D LEU* 3.3 19.5 - - + +
114D THR* 3.9 13.9 - - + -
229D LEU* 3.7 34.1 - - + -
232D GLY* 6.2 0.4 - - - -
237D VAL* 4.6 6.5 - - + -
239D MET* 1.3 77.9 - - - +
241D PHE* 1.3 70.1 + - - +
242D ALA* 3.5 4.7 + - + +
254D VAL* 4.5 9.6 - - + -
258D LEU* 4.4 12.8 - - + -
265D ILE* 4.0 16.2 - - + -
266D LYS 2.8 11.4 + - - +
267D ILE* 3.7 4.7 - - + +
268D ILE* 2.8 28.9 + - - +
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Residues in contact with PHE 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ILE* 4.1 14.6 - - + -
73D ARG* 3.7 32.5 - - + -
111D ALA* 3.6 26.2 - - + -
112D LEU 2.7 12.0 + - - +
113D ASP* 3.6 15.6 - - + +
114D THR 3.2 22.5 + - - -
239D MET* 3.7 21.8 - - + -
240D VAL* 1.3 73.0 - - - +
242D ALA* 1.3 63.5 + - - +
243D SER 3.4 1.4 + - - -
268D ILE* 3.4 34.8 - - + -
270D LYS* 3.9 10.5 - - + -
291D MET* 3.5 21.5 - - + -
325D ILE* 3.9 18.6 - - + -
360D MET* 4.5 0.2 - - - -
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Residues in contact with ALA 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D THR* 3.7 6.7 - - + -
240D VAL* 3.5 5.1 + - + -
241D PHE* 1.3 70.2 - - - +
243D SER* 1.3 64.1 + - - +
245D ILE* 3.4 25.3 - - + +
254D VAL* 4.2 22.4 - - + -
267D ILE* 4.5 13.9 - - + -
268D ILE 2.8 14.5 + - - +
269D SER* 4.6 0.9 - - - +
270D LYS* 2.9 28.9 + - - +
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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