Contacts of the helix formed by residues 373 - 381 (chain D) in PDB entry 1OKW
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 PRO 373 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321D HIS 3.9 18.4 - - - +
322D GLN* 5.9 0.4 - - - -
323D GLN* 4.7 16.2 - - - +
360D PHE* 4.2 10.8 - - + -
364D LEU* 4.4 5.6 - - + -
370D GLN* 6.1 1.1 - - - +
371D SER 3.5 8.3 - - - +
372D TRP* 1.3 89.7 - - + +
374D GLU* 1.3 59.7 + - - +
375D SER* 3.7 16.4 - - - +
376D LEU* 2.9 45.1 + - + +
377D ILE* 3.0 13.3 + - - +
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Residues in contact with GLU 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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372D TRP 3.8 1.8 + - - -
373D PRO* 1.3 68.7 - - - +
375D SER* 1.3 67.6 + - - +
377D ILE* 3.5 21.3 - - + +
378D ARG* 2.8 36.2 + - - +
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Residues in contact with SER 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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321D HIS* 3.3 31.3 + - - +
323D GLN* 5.2 2.1 + - - -
373D PRO* 3.7 14.7 - - - +
374D GLU* 1.3 75.8 - - - +
376D LEU* 1.3 56.4 + - - -
378D ARG* 3.3 10.1 + - - +
379D LYS* 3.1 28.1 + - - +
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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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318D TYR* 3.8 32.1 - - + +
321D HIS* 3.5 36.6 - - + +
360D PHE* 3.3 39.3 - - + -
372D TRP* 3.8 22.2 - - + -
373D PRO* 2.9 26.8 + - + +
375D SER* 1.3 71.5 + - - +
377D ILE* 1.3 55.4 + - - +
379D LYS* 4.5 5.8 - - + +
380D THR* 2.7 46.9 + - + +
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Residues in contact with ILE 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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372D TRP* 3.5 32.0 - - + +
373D PRO 3.0 14.2 + - - +
374D GLU* 3.5 23.8 - - + +
376D LEU* 1.3 76.2 - - - +
378D ARG* 1.3 56.4 - - - +
381D GLY* 2.9 28.7 + - - -
382D TYR 3.6 20.9 - - - +
383D THR* 4.3 11.9 - - + +
384D LEU* 4.5 10.3 - - + +
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Residues in contact with ARG 378 (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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374D GLU* 2.8 28.8 + - - +
375D SER* 3.5 11.7 - - - +
377D ILE* 1.3 76.2 - - - +
379D LYS* 1.3 62.8 + - - +
381D GLY* 3.9 4.5 + - - -
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Residues in contact with LYS 379 (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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179D HIS* 2.3 56.5 + - + +
180D GLU* 5.3 10.1 - - + +
183D HIS* 3.6 44.8 - - + +
317D GLN* 4.1 16.4 - - - +
318D TYR* 5.1 2.2 - - - -
321D HIS* 3.9 21.8 + - + +
375D SER 3.1 16.3 + - - +
376D LEU* 3.4 9.0 + - + +
378D ARG* 1.3 78.5 - - - +
380D THR* 1.3 64.9 + - + +
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Residues in contact with THR 380 (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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183D HIS* 4.0 16.6 - - + +
187D ARG* 3.3 23.7 + - - -
318D TYR* 3.7 34.8 - - + +
372D TRP* 3.6 10.1 - - + -
376D LEU* 2.7 32.0 + - + +
379D LYS* 1.3 78.3 - - + +
381D GLY* 1.3 62.8 + - - +
382D TYR* 3.2 34.6 + - - +
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Residues in contact with GLY 381 (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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377D ILE* 2.9 19.9 + - - -
378D ARG 3.9 4.0 + - - -
379D LYS 3.4 2.0 - - - -
380D THR* 1.3 78.9 + - - +
382D TYR* 1.3 65.4 - - - +
383D THR* 4.0 3.1 + - - +
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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