Contacts of the helix formed by residues 434 - 445 (chain B) in PDB entry 4J15
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 434 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A MET* 3.4 38.9 - - + +
602A GOL 3.7 21.4 + - - -
432B ILE* 3.3 3.7 - - + +
433B HIS* 1.3 79.6 - - + +
435B PRO* 1.4 73.7 - - - +
436B GLN* 3.2 14.1 + - - +
437B LEU* 3.1 26.5 + - + +
438B LEU* 3.0 24.1 + - - +
459B PHE* 4.9 0.9 - - - -
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Residues in contact with PRO 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A GLU* 4.3 5.2 - - + +
433B HIS 3.8 2.9 - - - +
434B ASP* 1.4 88.0 - - - +
436B GLN* 1.3 53.6 + - - +
438B LEU* 3.4 4.5 + - + +
439B THR* 2.7 38.0 + - - -
456B ILE* 4.2 10.5 - - + +
459B PHE* 3.5 39.5 - - + +
460B ARG* 3.6 40.8 - - + +
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Residues in contact with GLN 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B ASP* 3.2 11.7 + - - +
435B PRO* 1.3 74.6 - - - +
437B LEU* 1.3 65.6 + - - +
439B THR* 3.2 8.0 + - - -
440B GLU* 3.0 49.0 + - + +
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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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34A MET* 3.8 30.5 - - + -
36A GLN* 5.5 3.6 - - - +
404B MET* 4.1 16.8 - - - -
405B PRO* 4.4 10.3 - - + -
432B ILE* 3.9 21.1 - - + -
434B ASP* 3.1 15.0 + - - +
436B GLN* 1.3 74.3 - - - +
438B LEU* 1.3 65.1 + - - +
440B GLU* 3.4 21.7 + - + +
441B ARG* 3.3 35.1 + - + +
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Residues in contact with LEU 438 (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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401B PHE* 3.5 32.3 - - + +
402B TYR* 4.0 21.1 - - + -
432B ILE* 3.6 23.7 - - + +
434B ASP 3.0 18.1 + - - +
435B PRO* 3.6 4.7 - - + +
437B LEU* 1.3 76.4 - - - +
439B THR* 1.3 58.7 + - - +
441B ARG* 3.7 1.0 + - - +
442B ALA* 3.0 28.3 + - - +
455B TYR* 3.8 11.9 - - + +
456B ILE* 4.1 18.2 - - + -
459B PHE* 3.8 37.0 - - + -
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Residues in contact with THR 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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435B PRO 2.7 18.6 + - - -
436B GLN* 3.4 10.9 - - - -
437B LEU 3.2 0.2 - - - -
438B LEU* 1.3 74.9 - - - +
440B GLU* 1.3 65.5 + - + +
442B ALA* 3.2 3.6 + - - +
443B LEU* 3.0 25.5 + - + +
449B LEU* 3.7 35.6 - - + +
456B ILE* 3.7 19.5 - - + +
460B ARG* 4.9 4.0 + - - -
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Residues in contact with GLU 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 GLN* 3.0 47.3 + - + +
437B LEU* 3.4 28.4 - - + +
438B LEU 3.4 0.2 - - - -
439B THR* 1.3 75.7 - - + +
441B ARG* 1.3 53.7 + - + +
443B LEU* 3.0 17.2 - - + +
444B HIS* 2.9 31.3 + - - +
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Residues in contact with ARG 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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396B LEU* 3.4 45.1 + - - +
397B ALA* 5.6 1.6 - - - +
401B PHE* 3.4 20.9 + - - +
403B THR 4.8 0.2 + - - -
405B PRO* 4.6 8.5 - - + +
432B ILE* 3.5 21.3 - - + -
437B LEU* 3.4 29.6 - - + +
438B LEU 3.8 3.1 - - - +
440B GLU* 1.3 77.1 - - - +
442B ALA* 1.3 64.8 + - - +
444B HIS* 3.3 40.9 + - - +
445B HIS* 3.2 49.5 + - - -
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Residues in contact with ALA 442 (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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401B PHE* 3.6 23.3 - - + -
438B LEU 3.0 19.2 + - - +
439B THR* 3.2 5.8 + - - +
441B ARG* 1.3 75.6 - - - +
443B LEU* 1.3 64.0 + - - +
445B HIS 3.3 2.3 + - - -
446B GLY 3.2 4.0 + - - -
447B ILE* 3.0 30.9 + - + +
449B LEU* 3.9 8.5 - - + -
452B ILE* 3.8 23.6 - - + -
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Residues in contact with LEU 443 (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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439B THR* 3.0 17.9 + - + +
440B GLU* 3.0 15.7 - - + +
442B ALA* 1.3 72.1 - - - +
444B HIS* 1.3 62.1 + - - +
446B GLY* 2.9 19.3 + - - +
447B ILE 4.7 6.5 - - - +
449B LEU* 3.9 31.2 - - + -
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Residues in contact with HIS 444 (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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440B GLU 2.9 11.9 + - - +
441B ARG* 3.4 48.2 + - - +
442B ALA 3.2 0.2 - - - -
443B LEU* 1.3 77.7 - - - +
445B HIS* 1.3 66.4 + + - +
446B GLY 3.4 1.0 + - - -
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Residues in contact with HIS 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B LEU* 5.0 1.8 + - - +
397B ALA* 5.1 8.7 + - - -
399B ARG 3.2 27.3 + - - -
400B PRO* 4.0 1.7 + - + +
401B PHE* 3.6 31.9 + - + -
441B ARG* 3.2 34.4 + - - +
442B ALA 3.3 4.7 + - - +
443B LEU 3.1 0.4 - - - -
444B HIS* 1.3 90.6 - + + +
446B GLY* 1.3 61.8 + - - +
447B ILE* 3.4 11.8 + - + +
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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