Contacts of the strand formed by residues 313 - 318 (chain A) in PDB entry 3COG
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 313 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A GLN* 3.0 18.8 + - - +
190A PHE* 3.7 38.6 - - + -
213A TYR* 3.4 23.1 - - + +
291A TYR* 3.2 19.2 - - - -
311A THR* 3.3 11.2 + - - +
312A GLY* 1.3 77.3 - - - +
314A VAL* 1.3 58.1 + - - +
341A LEU* 3.7 23.1 - - + -
375A ARG* 3.5 35.2 - - + +
376A LEU 3.4 15.7 - - - +
377A SER* 3.7 23.1 - - - -
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Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLN* 3.8 0.2 - - - +
273A GLY* 3.5 23.8 - - - +
276A VAL* 4.3 6.7 - - + -
277A ALA* 4.1 8.3 - - + -
280A LEU* 4.0 25.6 - - + -
289A VAL* 4.1 21.1 - - + -
290A ILE 4.2 2.0 - - - -
291A TYR* 3.8 11.7 - - + -
312A GLY 3.8 9.6 - - - +
313A MET* 1.3 79.5 - - - +
315A THR* 1.3 64.6 + - - +
374A ILE 4.1 0.2 - - - +
375A ARG* 3.9 0.6 - - - -
376A LEU* 2.8 43.8 + - + +
378A VAL* 4.0 11.0 - - + -
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Residues in contact with THR 315 (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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162A PRO 2.7 30.0 + - - +
164A GLN* 3.3 12.1 + - - +
289A VAL* 3.5 3.5 - - - +
290A ILE* 2.6 65.0 + - + +
314A VAL* 1.3 74.4 - - - +
316A PHE* 1.3 63.1 + - - +
317A TYR* 5.2 0.2 - - + -
373A LEU* 3.8 25.6 - - + -
374A ILE 3.5 10.8 - - - +
375A ARG* 3.9 9.9 - - - +
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Residues in contact with PHE 316 (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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280A LEU* 3.8 22.2 - - + -
286A VAL* 3.8 29.6 - - + -
288A LYS 3.2 12.6 - - - +
289A VAL* 4.1 8.5 - - + -
290A ILE 4.6 0.2 - - - +
314A VAL 4.9 0.2 - - - -
315A THR* 1.3 78.8 - - - +
317A TYR* 1.3 72.4 + - - +
318A ILE* 4.1 12.6 - - + -
328A PHE* 3.7 26.9 - + - -
372A THR 3.6 0.3 - - - +
373A LEU* 3.5 3.3 - - - +
374A ILE* 2.7 81.4 + - + +
376A LEU* 3.9 21.3 - - + -
394A LEU* 4.4 7.0 - - + -
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Residues in contact with TYR 317 (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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163A THR* 4.9 2.6 - - - +
286A VAL* 3.7 5.2 - - - +
287A GLU* 2.8 40.9 + - + -
288A LYS* 2.8 38.0 + - + +
290A ILE* 3.6 26.5 - - + +
316A PHE* 1.3 79.3 - - - +
318A ILE* 1.3 61.9 + - - +
367A LEU 4.9 0.2 + - - -
368A GLY* 2.4 38.6 + - - -
370A SER* 3.4 21.5 - - - -
372A THR* 3.2 12.3 - - - +
373A LEU* 3.5 22.2 - - + +
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Residues in contact with ILE 318 (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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285A TRP 3.8 11.2 - - - +
287A GLU* 4.2 4.7 - - - +
316A PHE* 3.9 12.7 - - + -
317A TYR* 1.3 74.3 - - - +
319A LYS* 1.3 73.7 + - - +
320A GLY 3.8 0.9 + - - +
321A THR 4.4 0.2 - - - +
324A HIS* 3.7 26.5 - - + +
325A ALA* 3.8 24.9 - - + +
328A PHE* 3.7 16.6 - - + -
372A THR* 3.0 43.8 + - + +
374A ILE* 4.2 3.8 - - + -
394A LEU* 3.7 26.2 - - + -
397A ALA* 4.4 3.8 - - + -
398A HIS* 4.0 6.1 - - - +
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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