Contacts of the strand formed by residues 435 - 439 (chain A) in PDB entry 4CH9
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 GLY 435 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A GLY* 5.4 0.2 - - - -
433A SER 4.0 1.4 + - - -
434A VAL* 1.3 74.4 - - - +
436A VAL* 1.3 65.5 + - - +
445A ALA* 3.6 0.3 - - - -
446A VAL 2.8 35.8 + - - -
483A ALA 4.4 9.8 + - - +
485A VAL* 3.6 28.3 - - - -
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Residues in contact with VAL 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A GLY* 3.7 8.7 - - - -
389A ALA 3.4 42.8 - - - +
390A ALA* 3.9 5.6 - - + -
399A VAL* 4.0 34.8 - - + -
434A VAL* 4.7 2.2 - - + -
435A GLY* 1.3 80.0 - - - +
437A GLY* 1.3 59.8 + - - +
443A LEU* 4.2 7.0 - - + -
444A TYR 3.1 14.4 - - - +
445A ALA* 4.2 3.4 - - + -
485A VAL* 3.4 25.0 - - - +
486A GLY* 5.0 0.5 - - - -
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Residues in contact with GLY 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ALA* 5.2 2.5 - - - -
436A VAL* 1.3 78.2 - - - +
438A VAL* 1.3 64.0 + - - -
443A LEU* 3.7 2.5 - - - +
444A TYR* 2.8 36.6 + - - +
485A VAL* 4.2 2.3 - - - +
486A GLY* 5.5 1.1 - - - -
487A VAL* 4.1 9.0 - - - -
492A LEU* 4.0 17.4 - - - +
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Residues in contact with VAL 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ALA* 3.9 10.8 - - + -
391A VAL 3.4 26.0 - - - +
392A LEU* 3.8 27.4 - - + -
437A GLY* 1.3 75.0 - - - +
439A VAL* 1.3 67.5 + - - +
440A GLU 4.9 0.2 - - - +
441A GLY 4.5 6.1 - - - +
442A LYS 3.3 12.3 - - - +
443A LEU* 3.9 19.5 - - + -
487A VAL* 3.5 20.9 - - - +
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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
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437A GLY 4.2 0.6 + - - -
438A VAL* 1.3 79.5 - - - +
440A GLU* 1.3 85.2 + - + +
441A GLY 3.3 1.8 - - - -
442A LYS* 3.0 23.1 + - - +
444A TYR* 4.1 20.6 + - + -
487A VAL* 3.7 24.7 - - + -
490A GLY* 3.3 35.9 - - - +
492A LEU* 4.4 15.5 - - + +
512A PRO* 3.9 14.5 - - + +
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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