Contacts of the helix formed by residues 430 - 441 (chain B) in PDB entry 4OMC
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 ASP 430 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B LEU 3.8 3.1 - - - -
133B ASN* 2.6 35.5 + - - -
400B THR* 3.7 21.2 + - - +
401B SER* 4.9 0.6 - - - +
402B LYS* 2.8 32.0 + - + +
428B LEU 3.6 0.6 + - - -
429B LEU* 1.3 75.0 - - - +
431B ALA* 1.3 57.4 + - - +
433B ALA* 2.9 18.9 + - + +
434B MET* 2.9 33.2 + - - +
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Residues in contact with ALA 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B LEU 3.0 14.4 + - - +
133B ASN 3.5 11.4 - - - +
134B VAL* 3.7 14.1 - - + -
137B ALA* 4.0 10.9 - - + +
377B ILE* 4.0 35.4 - - + +
380B LEU* 4.6 5.2 - - + -
429B LEU 4.0 0.8 - - - -
430B ASP* 1.3 72.0 - - - +
432B GLY* 1.3 64.0 + - - +
434B MET* 3.1 1.8 + - - +
435B VAL* 3.0 27.5 + - - +
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Residues in contact with GLY 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ASN* 3.1 28.5 + - - -
136B ALA* 4.1 8.7 - - - -
137B ALA* 4.1 5.1 - - - +
140B GLN* 3.2 22.0 - - - +
430B ASP* 3.3 2.2 + - - -
431B ALA* 1.3 75.3 - - - +
433B ALA* 1.3 62.0 + - - +
435B VAL* 4.0 0.3 - - - +
436B ALA* 3.1 22.1 + - - +
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Residues in contact with ALA 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ASN* 4.1 1.0 - - - +
400B THR* 3.7 13.4 - - + +
402B LYS* 3.7 13.2 - - - +
430B ASP* 2.9 32.0 + - + +
432B GLY* 1.3 72.6 - - - +
434B MET* 1.3 65.9 + - - +
436B ALA* 3.7 5.4 - - - +
437B LEU* 3.0 27.7 + - - +
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Residues in contact with MET 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ILE* 4.2 15.3 - - + -
378B ILE* 4.7 5.8 - - + -
381B THR* 3.5 28.3 - - + +
393B MET* 3.9 19.3 - - - -
396B LEU* 3.7 28.1 - - + +
397B VAL* 3.8 25.4 - - + -
400B THR* 3.1 25.1 - - - +
429B LEU* 5.4 5.4 - - + -
430B ASP 2.9 22.6 + - - +
431B ALA* 3.1 9.8 + - - +
433B ALA* 1.3 77.0 - - - +
435B VAL* 1.3 57.0 + - - +
437B LEU* 3.9 1.4 - - - +
438B ALA* 3.0 29.6 + - - +
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Residues in contact with VAL 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ALA* 4.4 7.9 - - + -
140B GLN* 3.6 23.6 - - + +
142B TYR* 3.2 42.2 - - + -
380B LEU* 3.5 38.6 - - + +
381B THR* 4.1 3.1 - - - +
384B ALA* 3.8 9.0 - - + +
431B ALA 3.0 15.3 + - - +
434B MET* 1.3 74.7 - - - +
436B ALA* 1.3 67.9 + - - +
438B ALA* 3.6 3.6 + - - +
439B GLN* 3.3 22.7 + - - +
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Residues in contact with ALA 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B GLN* 3.8 18.4 - - - +
432B GLY 3.1 20.5 + - - +
433B ALA* 3.7 6.5 - - - +
435B VAL* 1.3 80.7 - - - +
437B LEU* 1.3 62.6 + - - +
438B ALA 3.3 0.2 + - - -
439B GLN* 3.4 17.5 + - - +
440B ASN* 4.1 6.4 + - - +
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Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B LEU* 3.6 22.7 - - + -
399B GLN* 3.8 28.7 - - + +
400B THR* 3.6 24.0 - - + -
433B ALA 3.0 17.4 + - - +
434B MET 4.1 2.7 - - - +
436B ALA* 1.3 76.2 - - - +
438B ALA* 1.3 64.1 + - - +
439B GLN 3.2 0.9 + - - -
440B ASN* 3.3 9.3 + - + -
441B TRP* 3.2 32.0 + - + +
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Residues in contact with ALA 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B THR* 3.7 32.8 - - + +
384B ALA* 4.1 3.6 - - + -
385B ASN* 2.8 31.1 + - + +
388B LEU* 4.1 4.7 - - + -
396B LEU* 4.0 12.7 - - + +
434B MET 3.0 19.2 + - - +
435B VAL 3.7 6.5 - - - +
436B ALA 3.2 0.2 - - - -
437B LEU* 1.3 77.4 - - - +
439B GLN* 1.3 59.8 + - - +
441B TRP* 3.2 10.2 + - - +
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Residues in contact with GLN 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B GLN* 3.8 15.6 - - - +
142B TYR* 3.2 37.8 + - - +
384B ALA* 4.1 16.8 - - + +
385B ASN* 4.6 4.3 + - - +
435B VAL 3.3 18.4 + - - +
436B ALA* 3.4 9.1 + - - +
437B LEU 3.2 0.6 - - - -
438B ALA* 1.3 77.7 - - - +
440B ASN* 1.3 69.3 + - - +
441B TRP 3.7 0.5 + - - +
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Residues in contact with ASN 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436B ALA 4.1 5.1 + - - +
437B LEU* 3.3 11.9 + - + +
439B GLN* 1.3 86.5 + - - +
441B TRP* 1.3 62.0 + - - +
442B THR* 3.4 8.3 + - - -
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Residues in contact with TRP 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B ASN* 3.9 10.9 + - - -
388B LEU* 3.6 24.5 - - + -
392B ASP* 2.8 30.4 + - + +
395B HIS* 3.6 29.8 - + + -
396B LEU* 3.6 21.5 - - + -
399B GLN* 3.7 36.6 - - - -
437B LEU* 3.2 21.7 + - + +
438B ALA* 3.2 19.3 + - - +
439B GLN 3.3 0.9 - - - +
440B ASN* 1.3 77.1 - - - +
442B THR* 1.3 78.1 + - - +
443B THR* 3.8 3.7 + - - -
444B VAL* 3.9 15.3 - - + -
483B ARG* 5.7 3.4 - - - -
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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