Contacts of the helix formed by residues 430 - 439 (chain B) in PDB entry 3C5R
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 THR 430 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-2B PRO* 4.9 10.1 - - + -
-1B PHE 3.9 12.6 - - - +
0B THR* 3.9 21.5 - - + -
428B GLY 4.4 0.7 - - - +
429B GLU* 1.3 74.9 - - - +
431B LEU* 1.3 65.1 + - - +
432B LEU* 3.3 11.8 + - - +
433B HIS* 2.9 46.5 + - + +
434B ILE* 3.1 18.2 + - - +
456B VAL* 4.4 15.0 - - + +
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Residues in contact with LEU 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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-1B PHE 4.8 2.2 + - - -
430B THR* 1.3 73.1 - - - +
432B LEU* 1.3 57.3 + - - +
434B ILE* 3.2 14.6 + - + +
435B ALA* 2.9 31.9 + - - +
443B SER* 6.3 1.1 - - - -
447B LEU* 3.8 33.7 - - + -
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Residues in contact with LEU 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B THR* 3.2 9.6 + - - +
431B LEU* 1.3 78.2 - - - +
433B HIS* 1.3 54.9 + - - +
435B ALA* 3.8 0.8 - - - -
436B SER* 2.7 46.0 + - - +
444B VAL* 4.1 27.1 - - + +
447B LEU* 3.7 16.2 - - + +
448B LEU* 3.9 19.5 - - + -
452B SER* 4.2 14.6 - - - -
453B ASP 4.0 7.9 - - - +
454B PRO* 3.8 28.9 - - + -
456B VAL* 5.2 1.6 - - + -
464B PRO* 3.8 14.6 - - + -
480B LEU* 4.1 12.3 - - + -
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Residues in contact with HIS 433 (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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428B GLY 4.1 5.4 - - - -
429B GLU* 3.9 13.5 - - + -
430B THR* 2.9 42.4 + - + +
432B LEU* 1.3 78.3 - - - +
434B ILE* 1.3 57.6 - - - +
436B SER* 3.1 4.9 + - - -
437B ILE* 2.9 38.2 + - + +
456B VAL* 3.4 34.2 + - + +
457B LYS 4.1 2.5 - - - -
458B ASP* 3.4 24.5 + - + -
462B TRP 2.9 28.3 + - - -
463B THR 4.1 2.5 - - - -
464B PRO* 3.8 19.6 - - + +
467B GLU* 4.6 7.2 - - + +
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Residues in contact with ILE 434 (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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425B ASN* 3.8 10.1 - - - +
427B ARG* 5.3 0.7 - - - +
429B GLU* 3.4 38.4 - - + +
430B THR 3.1 16.8 + - - +
431B LEU* 3.2 14.6 + - + +
433B HIS* 1.3 76.2 - - - +
435B ALA* 1.3 57.8 + - - +
437B ILE* 3.3 12.5 + - + +
438B LYS* 2.9 24.6 + - - -
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Residues in contact with ALA 435 (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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431B LEU* 2.9 18.8 + - + +
432B LEU* 4.1 2.5 - - - +
434B ILE* 1.3 77.9 - - - +
436B SER* 1.3 57.7 + - - +
437B ILE 3.4 0.2 - - - -
438B LYS* 3.3 1.5 + - - +
439B GLY* 2.8 6.9 - - - -
440B ASP* 2.6 35.8 + - + +
443B SER* 3.8 25.4 - - - -
444B VAL* 3.8 20.3 - - + +
447B LEU* 4.7 2.9 - - + -
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Residues in contact with SER 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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432B LEU* 2.7 24.0 + - - +
433B HIS 3.1 3.8 + - - -
435B ALA* 1.3 73.0 - - - +
437B ILE* 1.3 65.8 + - - +
438B LYS 3.2 0.2 - - - -
439B GLY* 3.7 0.7 - - - -
444B VAL* 3.9 9.5 - - - +
464B PRO* 3.3 38.8 - - - +
467B GLU* 4.4 0.9 - - - -
468B ALA* 3.8 11.1 - - - +
473B HIS* 3.0 21.7 - - - -
476B VAL* 4.0 13.2 - - - +
480B LEU* 3.9 8.0 - - - +
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Residues in contact with ILE 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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537A GLU* 6.5 0.7 - - + -
538A SER* 3.6 23.8 - - - +
429B GLU* 4.7 19.5 - - + +
433B HIS* 2.9 25.8 + - + +
434B ILE* 3.4 12.8 - - + +
436B SER* 1.3 73.5 - - - +
438B LYS* 1.3 55.2 + - - +
467B GLU* 3.4 38.5 - - + +
471B HIS* 3.9 23.8 - - + +
473B HIS* 2.8 23.6 + - - -
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Residues in contact with LYS 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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434B ILE 2.9 13.8 + - - -
435B ALA* 3.3 5.4 + - - +
436B SER 3.2 2.4 - - - -
437B ILE* 1.3 78.6 - - - +
439B GLY* 1.3 54.0 + - - +
440B ASP* 3.9 3.8 - - - +
473B HIS* 3.5 6.2 + - - -
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Residues in contact with GLY 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 ALA 2.8 12.6 - - - -
436B SER 3.7 2.0 - - - -
438B LYS* 1.3 67.4 + - - -
440B ASP* 1.3 61.2 + - - -
441B ILE* 3.3 14.5 + - - +
473B HIS* 3.0 36.0 + - - -
476B VAL* 4.1 10.0 - - - +
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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