Contacts of the helix formed by residues 435 - 445 (chain B) in PDB entry 3FO5
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 435 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434B VAL* 1.3 75.8 - - - +
436B ALA* 1.3 57.0 + - - +
437B ALA* 3.1 32.4 + - - +
438B GLN* 3.2 15.6 + - + +
439B ALA* 2.9 26.0 + - - +
536B ARG* 2.6 25.0 + - - -
538B GLY 5.5 0.3 - - - +
539B ASP* 5.8 0.5 - - - -
540B GLN* 4.0 38.4 + - - +
541B LEU 4.8 0.7 - - - +
542B THR* 3.4 0.2 - - - -
584B ARG* 5.5 2.1 + - - +
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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
----------------------------------------------------------
435B ASP* 1.3 75.0 + - - +
437B ALA* 1.3 57.8 + - - +
439B ALA* 3.2 3.5 + - - +
440B PHE* 2.8 30.0 + - - +
504B TYR* 3.6 26.2 - - + -
534B LEU* 4.1 3.9 - - + +
535B TRP 4.6 0.4 - - - -
536B ARG* 3.9 27.9 - - + +
541B LEU 5.0 1.2 + - - -
542B THR* 2.9 32.2 + - + +
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Residues in contact with ALA 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ASP* 3.1 13.3 + - - +
436B ALA* 1.3 77.9 - - - +
438B GLN* 1.3 61.5 + - - +
440B PHE* 3.3 5.1 - - - +
441B LEU* 3.2 29.1 + - + +
496B LYS* 4.0 12.3 - - - +
504B TYR* 3.7 26.9 + - - +
536B ARG* 4.0 4.1 - - - +
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Residues in contact with GLN 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B VAL* 5.7 2.2 - - + -
435B ASP* 3.2 22.3 + - + +
437B ALA* 1.3 76.9 - - - +
439B ALA* 1.3 64.6 + - - +
440B PHE 3.3 0.2 + - - -
441B LEU* 3.3 15.3 + - - +
442B LEU* 3.0 38.1 + - + +
583B ASN 3.2 18.8 + - - -
584B ARG* 3.1 25.1 - - - +
585B ASN* 4.9 0.9 - - - -
586B ASP 2.8 31.8 + - - +
589B PRO* 3.8 14.7 - - - +
590B SER* 5.3 2.8 + - - -
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Residues in contact with ALA 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B VAL* 3.9 19.8 - - + +
435B ASP 2.9 14.0 + - - +
436B ALA* 3.6 10.5 - - - +
438B GLN* 1.3 75.5 - - - +
440B PHE* 1.3 56.9 + - - +
442B LEU* 3.8 0.8 - - - +
443B LEU* 2.9 37.1 + - + +
534B LEU* 3.7 18.2 - - + -
542B THR* 4.7 4.7 - - + -
544B VAL* 5.0 0.2 - - + -
580B LEU* 3.9 22.9 - - + -
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Residues in contact with PHE 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ALA 2.8 13.5 + - - +
437B ALA* 3.3 11.4 - - - +
438B GLN 3.2 0.2 - - - -
439B ALA* 1.3 74.0 - - - +
441B LEU* 1.3 66.7 + - + +
444B SER* 2.6 40.7 + - - -
468B ASP* 5.2 2.0 - - - -
494B ARG* 3.7 37.7 - - + -
495B ARG 3.7 31.9 - - - -
496B LYS* 3.8 14.1 - - + -
504B TYR* 3.3 38.1 - + + -
505B VAL 3.7 15.0 - - - -
506B ILE* 3.7 12.0 - - + +
534B LEU* 3.5 9.4 - - + +
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Residues in contact with LEU 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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437B ALA* 3.2 15.5 + - + +
438B GLN* 3.3 13.9 + - - +
440B PHE* 1.3 85.5 - - + +
442B LEU* 1.3 65.0 + - - +
444B SER* 3.4 11.7 + - - -
445B ASP* 3.5 15.1 + - - +
494B ARG* 4.0 23.8 + - - +
589B PRO* 3.5 27.3 - - + +
590B SER* 3.5 40.4 - - - +
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Residues in contact with LEU 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B VAL* 6.2 0.7 - - + -
438B GLN* 3.0 33.6 + - + +
439B ALA* 3.8 4.0 - - - +
441B LEU* 1.3 77.1 - - - +
443B LEU* 1.3 60.4 + - - +
445B ASP* 3.9 15.9 + - - +
448B GLN* 4.6 10.6 - - - +
452B TRP* 5.4 0.5 + - - -
579B PHE* 3.8 28.4 - - + +
580B LEU* 3.7 37.9 - - + +
583B ASN* 3.7 41.1 - - + +
586B ASP* 5.3 0.9 - - + +
589B PRO* 4.0 21.3 - - + -
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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
----------------------------------------------------------
439B ALA 2.9 21.3 + - - +
442B LEU* 1.3 76.8 - - - +
444B SER* 1.3 62.0 - - - +
445B ASP* 3.3 5.9 + - - -
446B LEU* 4.5 8.1 + - - +
449B ARG* 6.0 0.9 - - - +
452B TRP* 3.9 35.8 - - + +
506B ILE* 3.6 19.9 - - + +
532B PHE* 4.0 30.8 - - + -
534B LEU* 3.9 27.4 - - + -
544B VAL* 4.3 8.3 - - + -
576B CYS* 3.9 13.5 - - - -
579B PHE* 4.7 2.2 - - + -
580B LEU* 4.0 22.2 - - + -
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Residues in contact with SER 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B PHE* 2.6 24.0 + - - -
441B LEU* 3.4 7.3 + - - -
442B LEU 3.5 0.2 - - - -
443B LEU* 1.3 76.0 - - - +
445B ASP* 1.3 58.1 + - - +
446B LEU* 3.2 10.4 + - - +
472B TYR* 4.1 9.2 + - - -
492B ALA* 5.5 3.5 - - - +
494B ARG* 3.0 50.2 + - - -
506B ILE* 3.6 24.5 - - - +
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Residues in contact with ASP 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B LEU 3.5 15.2 + - - +
442B LEU 3.9 6.4 + - - +
443B LEU 3.3 3.8 - - - +
444B SER* 1.3 73.8 + - - +
446B LEU* 1.3 58.2 + - - +
447B ARG* 3.1 40.0 + - - +
448B GLN* 3.0 44.7 + - + +
449B ARG* 3.9 1.9 + - - +
472B TYR* 4.4 5.5 + - - -
494B ARG* 6.1 0.7 - - - +
592B GLN* 3.2 23.7 - - - +
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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