Contacts of the helix formed by residues 437 - 444 (chain B) in PDB entry 3F8J
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 PHE 437 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435B TRP* 4.0 0.3 - - - +
436B ARG* 1.3 107.3 - - + +
438B ARG* 1.3 65.5 + - - +
439B VAL* 4.0 18.8 - - + -
440B GLN* 2.8 30.9 + - - +
441B VAL* 3.4 9.0 + - - +
557B ASN* 3.6 5.4 - - - +
612B PRO* 3.5 25.6 - - + -
615B TYR* 3.4 48.7 - + - -
409F C 3.6 22.9 - - - +
410F T 3.9 29.8 - - - -
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Residues in contact with ARG 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B PHE* 1.3 71.9 - - - +
439B VAL* 1.3 57.6 + - + +
441B VAL* 3.0 15.4 + - - +
442B SER* 2.9 30.2 + - - -
447B HIS* 3.3 16.4 - - - -
449B PRO 2.8 24.0 + - - -
450B HIS* 3.2 29.4 + - + +
451B VAL 3.3 5.1 + - - -
452B ALA 2.8 26.2 + - - -
466B VAL* 4.1 22.1 - - - +
540B VAL* 5.9 0.2 - - - -
542B ASN* 4.7 3.4 - - - +
557B ASN* 3.7 24.1 - - - +
407F 5CM 4.0 7.9 + - - +
408F G 3.2 44.4 + - - +
409F C 2.8 17.5 + - - +
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Residues in contact with VAL 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B PHE* 4.0 17.9 - - + +
438B ARG* 1.3 77.1 - - + +
440B GLN* 1.3 62.9 - - + +
442B SER* 3.4 9.7 + - - -
443B GLU* 3.0 42.8 + - + +
450B HIS* 3.9 25.6 - - + -
612B PRO* 6.0 2.2 - - + -
409F C 4.7 2.2 + - - +
427G G 5.2 6.3 - - - +
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Residues in contact with GLN 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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435B TRP* 3.8 17.6 - - + -
436B ARG 3.3 5.5 + - - -
437B PHE* 2.8 40.8 + - + +
439B VAL* 1.3 80.8 - - + +
441B VAL* 1.3 65.3 + - - +
442B SER 3.1 0.2 - - - -
443B GLU* 3.3 13.9 + - - +
444B SER* 3.1 22.2 + - - -
610B GLN* 2.9 37.1 + - - +
611B TYR 3.3 14.5 + - - -
612B PRO* 3.5 23.9 - - + +
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Residues in contact with VAL 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B TRP* 3.6 29.2 - - + -
437B PHE 3.6 13.7 - - - +
438B ARG* 3.0 13.8 + - - +
440B GLN* 1.3 76.5 - - - +
442B SER* 1.3 61.4 + - - +
444B SER* 2.6 23.2 + - - -
445B GLY 3.5 2.9 + - - -
446B VAL* 4.1 9.9 - - + -
447B HIS* 3.5 34.0 + - + +
540B VAL* 4.2 15.3 - - + -
557B ASN* 3.7 24.2 - - + -
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Residues in contact with SER 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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438B ARG 2.9 12.5 + - - -
439B VAL* 3.5 11.9 - - - -
441B VAL* 1.3 78.0 - - - +
443B GLU* 1.3 59.3 + - - +
445B GLY* 2.9 21.0 + - - -
447B HIS 3.1 15.4 + - - -
448B ARG* 2.7 34.3 + - - +
449B PRO 3.3 8.0 + - - -
450B HIS* 3.5 10.6 - - - +
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Residues in contact with GLU 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 VAL* 3.0 33.6 + - + +
440B GLN* 3.3 14.7 + - - +
442B SER* 1.3 76.2 - - - +
444B SER* 1.3 59.8 + - - +
445B GLY* 3.2 0.9 + - - -
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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
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426B ILE* 3.7 18.7 - - - +
429B VAL* 4.7 7.6 - - - +
435B TRP* 3.6 23.9 - - - -
440B GLN 3.1 11.1 + - - -
441B VAL 2.6 21.1 + - - -
442B SER 3.1 0.4 - - - -
443B GLU* 1.3 76.7 - - - +
445B GLY* 1.3 56.7 + - - +
446B VAL* 3.2 20.6 + - - +
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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