Contacts of the strand formed by residues 373 - 377 (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 LEU 373 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D PRO* 4.7 5.8 - - + -
163D THR* 4.3 13.5 - - + -
290D ILE* 4.9 0.9 - - + -
315D THR* 3.4 33.7 - - + -
316D PHE 3.6 4.9 - - - -
317D TYR* 3.2 44.0 - - + +
350D LEU* 3.3 12.5 - - - +
351D PRO* 3.3 37.0 - - + +
368D GLY 3.4 7.6 - - - +
369D ILE* 4.3 9.2 - - + -
370D SER* 3.4 20.6 + - - +
372D THR* 1.3 75.7 - - - +
374D ILE* 1.3 68.5 + - - +
375D ARG 4.3 0.2 - - - +
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Residues in contact with ILE 374 (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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315D THR* 3.5 4.3 - - - +
316D PHE* 2.8 72.0 + - + +
318D ILE* 4.0 17.9 - - + -
325D ALA* 4.2 13.2 - - + +
328D PHE* 3.6 31.0 - - + -
329D LEU* 4.3 8.5 - - + -
349D GLU 3.5 12.1 - - - +
350D LEU* 4.1 13.9 - - + -
372D THR 3.9 4.3 - - - +
373D LEU* 1.3 79.1 - - - +
375D ARG* 1.3 62.4 + - - +
376D LEU* 4.1 16.2 - - + -
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Residues in contact with ARG 375 (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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161D ASN* 2.9 28.0 + - - +
162D PRO* 4.0 11.4 - - + -
164D GLN* 5.6 0.9 - - - +
190D PHE* 4.5 3.4 - - + -
313D MET* 3.4 23.5 - - + +
314D VAL 3.8 3.4 - - - +
315D THR* 3.9 17.3 - - - +
339D GLU 4.9 0.2 - - - -
340D SER 3.1 18.4 + - - +
341D LEU* 3.8 10.0 - - - +
348D ALA* 3.5 2.9 - - - -
349D GLU* 3.0 66.5 + - + +
351D PRO* 4.0 17.5 - - + +
355D THR* 4.0 1.4 + - - -
356D HIS* 4.4 0.4 - - - -
373D LEU* 4.8 0.7 - - + -
374D ILE* 1.3 72.8 - - - +
376D LEU* 1.3 66.1 + - - +
377D SER* 4.3 1.2 + - - +
607D NO3 2.7 44.4 + - - -
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Residues in contact with LEU 376 (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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276D VAL* 4.0 23.1 - - + -
280D LEU* 4.0 4.9 - - + -
313D MET* 3.3 13.5 - - - +
314D VAL* 2.8 41.4 + - + +
316D PHE* 3.9 23.1 - - + -
328D PHE* 4.8 2.7 - - + -
335D PHE* 3.8 17.7 - - + -
347D LEU 3.5 1.6 - - - +
348D ALA* 3.5 30.3 - - + -
374D ILE* 4.1 10.3 - - + -
375D ARG* 1.3 78.1 - - - +
377D SER* 1.3 58.9 + - - +
378D VAL* 3.8 7.4 - - + -
390D LEU* 3.9 23.1 - - + -
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Residues in contact with SER 377 (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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213D TYR* 4.6 1.6 + - - -
269D HIS* 5.8 0.2 - - - -
313D MET* 3.7 19.6 - - - -
335D PHE* 4.8 0.4 - - - -
340D SER 4.7 1.3 - - - -
341D LEU* 3.5 15.4 - - - +
342D GLY* 2.9 27.0 + - - -
343D GLY 4.5 2.8 + - - -
345D GLU 3.8 3.8 + - - +
346D SER* 3.2 4.3 - - - -
347D LEU* 2.9 45.7 + - - +
375D ARG* 5.5 0.9 - - - +
376D LEU* 1.3 71.1 - - - +
378D VAL* 1.3 66.1 + - - +
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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