Contacts of the strand formed by residues 313 - 318 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164D GLN* 3.0 25.0 + - - +
190D PHE* 3.9 29.4 - - + -
213D TYR* 3.5 26.5 - - + +
291D TYR* 3.2 18.2 - - - -
311D THR* 3.3 9.7 + - - +
312D GLY* 1.3 75.8 - - - +
314D VAL* 1.3 59.5 + - - +
341D LEU* 3.6 35.0 - - + -
375D ARG* 3.4 37.2 - - + +
376D LEU 3.3 13.9 - - - +
377D SER* 3.7 15.5 - - - -
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Residues in contact with VAL 314 (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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164D GLN* 3.8 0.7 - - - +
273D GLY* 3.6 23.3 - - - +
276D VAL* 4.2 7.0 - - + -
277D ALA* 4.0 9.9 - - + -
280D LEU* 3.9 25.6 - - + -
289D VAL* 4.0 21.3 - - + -
290D ILE 4.2 3.4 - - - +
291D TYR* 3.7 11.7 - - + -
312D GLY 3.9 9.6 - - - +
313D MET* 1.3 78.1 - - - +
315D THR* 1.3 62.6 + - - +
316D PHE* 4.2 0.5 + - - -
374D ILE 4.1 0.5 - - - +
375D ARG* 3.8 0.8 - - - -
376D LEU* 2.8 46.6 + - + +
378D VAL* 4.0 10.8 - - + -
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Residues in contact with THR 315 (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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162D PRO 2.7 29.0 + - - +
164D GLN* 3.2 15.3 + - - +
289D VAL* 3.6 3.6 - - - +
290D ILE* 2.7 57.3 + - + +
314D VAL* 1.3 73.9 - - - +
316D PHE* 1.3 64.0 + - - +
373D LEU* 3.4 39.0 - - + -
374D ILE 3.5 4.0 - - - +
375D ARG* 3.9 10.0 - - - +
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Residues in contact with PHE 316 (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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280D LEU* 3.7 26.0 - - + -
286D VAL* 3.9 22.9 - - + -
288D LYS 3.1 14.1 - - - +
289D VAL* 4.1 13.0 - - + +
290D ILE* 4.6 0.7 - - - +
314D VAL 4.7 0.7 - - - -
315D THR* 1.3 79.1 - - - +
317D TYR* 1.3 75.0 + - - +
318D ILE* 4.1 9.9 - - + -
328D PHE* 3.9 19.1 - + - -
372D THR 3.6 0.3 - - - +
373D LEU* 3.6 2.9 - - - +
374D ILE* 2.8 85.1 + - + +
376D LEU* 3.9 23.6 - - + -
394D LEU* 4.5 4.5 - - + -
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Residues in contact with TYR 317 (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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163D THR* 4.9 1.9 - - - +
286D VAL* 3.7 5.0 - - - +
287D GLU* 2.8 43.2 + - + +
288D LYS* 2.8 37.8 + - + +
290D ILE* 3.9 20.6 - - + +
316D PHE* 1.3 75.5 - - - +
318D ILE* 1.3 62.6 + - - +
367D LEU 4.9 0.5 + - - -
368D GLY* 2.5 33.2 + - - -
370D SER* 3.4 26.9 - - - -
372D THR* 3.3 12.3 - - - +
373D LEU* 3.2 27.1 - - + +
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Residues in contact with ILE 318 (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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285D TRP 3.7 12.8 - - - +
287D GLU* 4.2 3.6 - - - +
316D PHE* 3.9 7.9 - - + -
317D TYR* 1.3 75.6 - - - +
319D LYS* 1.3 75.4 + - - +
320D GLY 3.8 0.3 + - - +
321D THR 4.4 0.2 - - - +
324D HIS* 3.6 26.7 - - + +
325D ALA* 3.9 22.2 - - + +
328D PHE* 3.7 20.2 - - + -
372D THR* 3.0 42.4 + - + +
374D ILE* 4.0 9.9 - - + -
394D LEU* 3.9 19.3 - - + -
397D ALA* 4.4 7.0 - - + -
399D PRO* 4.2 3.6 - - + -
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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