Contacts of the strand formed by residues 301 - 305 (chain D) in PDB entry 2G1T
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 LEU 301 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D TRP* 4.9 2.2 - - + -
287D ALA* 3.6 27.6 - - + +
290D MET* 4.0 32.2 + - + +
291D LYS* 3.2 45.3 + - + +
293D ILE 5.3 1.0 + - - -
299D VAL 3.7 2.8 + - - -
300D GLN* 1.3 80.9 - - - +
302D LEU* 1.3 57.1 + - - +
303D GLY* 3.4 26.9 - - - +
304D VAL* 4.1 13.5 - - + -
313D ILE* 3.6 22.2 - - + -
314D ILE 3.5 9.6 - - - +
315D THR* 4.2 5.8 - - + -
382D PHE* 5.2 4.1 - - + -
387D LEU* 6.3 0.2 - - + -
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Residues in contact with LEU 302 (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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234D LYS 4.9 0.9 - - - +
235D TRP* 3.5 15.2 - - - +
237D MET* 4.6 1.9 - - - +
261D TRP* 4.0 34.0 - - + -
266D LEU* 4.5 9.0 - - + -
268D VAL* 3.7 30.3 - - + -
291D LYS* 3.8 8.2 - - - +
300D GLN* 3.8 30.1 - - + +
301D LEU* 1.3 74.1 - - - +
303D GLY* 1.3 58.4 + - - +
314D ILE* 2.8 16.2 + - + +
315D THR 3.8 1.6 - - - -
316D GLU* 3.8 29.8 - - + +
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Residues in contact with GLY 303 (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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235D TRP* 3.1 20.0 - - - -
237D MET* 3.9 9.2 - - - -
301D LEU* 3.4 5.7 - - - +
302D LEU* 1.3 80.3 - - - +
304D VAL* 1.3 69.9 + - - +
314D ILE* 2.8 33.3 + - - +
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Residues in contact with VAL 304 (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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235D TRP* 3.0 39.0 + - + +
236D GLU* 3.6 5.5 - - + +
237D MET* 2.7 29.0 + - - +
283D PHE* 4.0 16.2 - - + -
284D LEU* 3.8 20.0 - - + -
287D ALA* 4.4 6.3 - - + -
301D LEU* 4.1 10.3 - - + -
303D GLY* 1.3 80.6 - - - +
305D CYS* 1.3 61.0 + - - +
306D THR* 4.2 4.6 + - + +
312D TYR 3.2 10.3 - - - +
313D ILE* 3.9 19.5 - - + -
314D ILE* 4.0 2.2 - - - +
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Residues in contact with CYS 305 (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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237D MET* 3.4 30.5 - - - +
238D GLU 3.8 15.0 - - - -
239D ARG* 3.9 17.7 - - + +
242D ILE* 4.6 3.4 - - - -
304D VAL* 1.3 74.7 - - - +
306D THR* 1.3 61.5 + - - +
307D ARG 3.9 1.3 - - - +
308D GLU 5.3 3.8 - - - +
311D PHE* 3.2 11.3 - - - +
312D TYR* 3.0 46.0 + - + +
314D ILE* 4.0 17.9 - - - -
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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