Contacts of the helix formed by residues 437 - 444 (chain A) in PDB entry 3F8I
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435A TRP* 4.1 0.9 - - - +
436A ARG* 1.3 114.3 - - + +
438A ARG* 1.3 65.5 + - - +
439A VAL* 4.0 18.4 - - + -
440A GLN* 2.9 25.4 + - - +
441A VAL* 3.5 8.1 + - - +
557A ASN* 3.7 4.9 - - - +
612A PRO* 3.4 25.8 - - + -
615A TYR* 3.5 43.5 - + - -
409D C 3.6 24.0 - - - +
410D T 4.2 27.4 - - - -
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Residues in contact with ARG 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A PHE* 1.3 68.1 - - - +
439A VAL* 1.3 62.9 + - + +
441A VAL* 2.8 31.3 + - - +
442A SER* 3.0 15.1 + - - -
447A HIS* 3.7 14.7 - - - -
449A PRO 3.4 17.4 + - - -
450A HIS* 3.5 19.8 + - - +
451A VAL 3.2 14.3 + - - -
452A ALA 2.7 28.9 + - - -
466A VAL* 3.7 24.5 - - - +
540A VAL* 5.8 1.1 - - - -
542A ASN* 5.1 1.1 - - - +
557A ASN* 3.9 23.2 - - - +
407D 5CM 4.3 0.6 - - - +
408D G 2.8 55.7 + - - +
409D C 2.9 17.4 + - - +
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Residues in contact with VAL 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A PHE* 4.0 18.2 - - + -
438A ARG* 1.3 75.1 - - + +
440A GLN* 1.3 64.3 - - + +
442A SER* 3.4 10.5 + - - -
443A GLU* 3.1 40.5 + - + +
450A HIS* 4.2 22.7 - - + -
612A PRO* 5.8 2.7 - - + -
409D C 4.8 1.1 + - - -
427E G 5.7 4.3 - - - +
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Residues in contact with GLN 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A TRP* 3.8 23.8 - - + +
436A ARG 3.3 6.4 + - - -
437A PHE* 2.9 33.8 + - - +
438A ARG 3.0 0.4 - - - -
439A VAL* 1.3 81.5 - - + +
441A VAL* 1.3 65.3 + - - +
443A GLU* 3.5 16.5 + - - +
444A SER* 3.4 16.8 + - - -
610A GLN* 3.4 19.6 + - - +
611A TYR 3.3 26.7 + - - -
612A PRO* 3.4 31.1 - - + +
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Residues in contact with VAL 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A TRP* 3.8 30.3 - - + -
437A PHE 3.7 13.7 - - - +
438A ARG* 2.8 18.7 + - - +
440A GLN* 1.3 77.1 - - - +
442A SER* 1.3 62.3 + - - +
444A SER* 2.7 23.7 + - - -
445A GLY 3.6 3.1 + - - -
446A VAL* 4.2 3.4 - - + -
447A HIS* 3.6 33.1 + - + +
540A VAL* 4.1 19.7 - - + -
557A ASN* 3.9 20.6 - - + -
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Residues in contact with SER 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A ARG 3.0 11.5 + - - -
439A VAL* 3.4 11.7 - - - -
441A VAL* 1.3 78.3 - - - +
443A GLU* 1.3 57.5 + - - +
445A GLY* 2.9 22.0 + - - -
447A HIS 3.2 14.4 + - - -
448A ARG* 2.8 33.6 + - - -
449A PRO 3.5 6.8 + - - -
450A HIS* 3.8 11.3 - - - +
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Residues in contact with GLU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A HIS* 6.0 0.2 + - - -
439A VAL* 3.1 25.1 + - - +
440A GLN* 3.9 16.6 - - - +
441A VAL 3.4 0.4 - - - -
442A SER* 1.3 77.5 - - - +
444A SER* 1.3 59.9 + - - +
445A GLY 3.4 0.7 + - - -
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Residues in contact with SER 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A ILE* 3.6 19.9 - - - +
429A VAL* 4.7 10.0 - - - +
435A TRP* 3.7 22.6 - - - -
440A GLN 3.4 9.4 + - - -
441A VAL 2.7 21.1 + - - -
443A GLU* 1.3 78.9 - - - +
445A GLY* 1.3 55.6 + - - +
446A VAL* 3.1 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