Contacts of the strand formed by residues 437 - 440 (chain A) in PDB entry 3H0G
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 ARG 437 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A SER 5.7 2.2 - - - +
3A GLY* 4.5 25.1 - - - +
4A ILE* 5.4 13.7 - - - +
383A PRO* 4.9 19.8 - - + +
384A GLU 4.4 1.8 - - - +
385A THR* 3.2 43.3 + - + +
386A VAL 4.3 0.4 - - - +
412A ILE* 2.7 61.2 + - + +
413A ARG 5.8 0.2 - - - -
435A GLY 5.2 0.4 - - - +
436A TRP* 1.3 76.1 - - - +
438A VAL* 1.3 67.9 + - - +
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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
----------------------------------------------------------
383A PRO* 2.6 27.8 - - - +
384A GLU* 3.1 12.9 + - - +
386A VAL* 4.5 2.4 - - + +
394A LEU* 3.5 31.0 - - + +
398A VAL* 4.7 7.6 - - + -
408A ALA* 4.8 6.1 - - + -
410A TYR 4.1 9.4 - - - +
411A ILE* 3.7 23.8 - - + -
412A ILE* 4.5 0.9 - - - +
432A LEU* 3.7 29.6 - - + -
436A TRP* 4.2 4.9 - - - +
437A ARG* 1.3 82.4 - - - +
439A GLU* 1.3 65.7 + - - +
440A ARG* 3.7 3.7 + - + +
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Residues in contact with GLU 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A PHE* 4.7 11.9 - - - -
381A THR* 3.6 23.1 - - + +
383A PRO* 3.6 33.7 - - + +
408A ALA* 3.0 12.9 - - - +
409A LYS* 2.6 32.5 + - + +
410A TYR* 3.3 38.8 + - - +
412A ILE* 4.0 21.8 - - + +
438A VAL* 1.3 74.2 - - - +
440A ARG* 1.3 60.7 + - - +
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Residues in contact with ARG 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A THR* 2.7 29.6 + - - +
382A TYR* 2.8 48.0 + - + +
383A PRO 4.4 2.2 - - - +
384A GLU* 3.3 25.9 + - - -
394A LEU* 6.0 3.8 - - + -
397A LEU* 4.3 26.8 - - + +
407A GLY 4.0 0.4 - - - +
408A ALA* 3.6 11.4 - - + -
409A LYS* 5.0 2.3 - - - +
438A VAL* 3.7 5.7 + - + +
439A GLU* 1.3 74.1 - - - +
441A HIS* 1.3 72.1 + - - +
443A ARG* 2.9 60.8 - - - +
444A ASP 5.1 1.0 + - - -
446A ASP* 3.4 4.8 + - - +
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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