Contacts of the strand formed by residues 442 - 446 (chain A) in PDB entry 5I35
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 VAL 442 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A THR* 4.1 13.7 - - + +
316A LEU* 4.0 20.4 - - + -
319A ASP* 4.3 7.4 - - + +
320A LEU* 4.9 5.8 - - + -
357A MSE 4.3 15.0 - - + -
358A LYS 3.3 10.8 - - - +
359A ILE* 4.3 9.6 - - + -
408A TYR* 3.6 3.3 - - - -
437A LEU 3.6 18.4 - - - +
438A CYS* 3.5 2.4 - - - +
439A SER* 2.9 43.9 + - - +
441A HIS* 1.3 86.0 - - - +
443A LEU* 1.3 65.1 + - - +
444A THR* 3.8 9.6 - - - +
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Residues in contact with LEU 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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356A ALA 3.7 2.1 - - - +
358A LYS* 2.8 47.2 + - + +
408A TYR* 3.6 28.2 - - + +
411A GLU* 3.1 38.1 - - + +
412A ALA* 3.6 33.2 - - + -
415A ALA* 5.8 1.3 - - + -
433A ILE* 4.3 13.7 - - + -
438A CYS* 3.9 12.6 - - + -
439A SER 5.6 0.2 - - - +
442A VAL* 1.3 75.2 - - - +
444A THR* 1.3 58.8 + - - +
445A THR* 4.2 8.7 + - + +
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Residues in contact with THR 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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355A VAL* 3.9 20.6 - - + -
356A ALA 3.4 9.4 - - - +
357A MSE 3.5 28.8 - - + +
433A ILE* 3.6 3.8 - - - -
434A VAL* 2.9 34.7 + - + -
437A LEU* 2.9 42.9 + - + +
438A CYS* 3.3 12.8 - - - -
442A VAL* 3.8 3.5 - - - +
443A LEU* 1.3 72.3 - - - +
445A THR* 1.3 63.2 + - - +
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Residues in contact with THR 445 (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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355A VAL* 3.4 6.6 - - - +
356A ALA 2.8 34.1 + - - -
415A ALA* 5.7 1.1 - - + -
431A PRO* 4.1 17.2 - - + +
432A GLU 3.3 10.1 - - - +
433A ILE* 3.6 30.3 - - + -
434A VAL* 4.4 0.7 - - - -
443A LEU* 4.2 11.1 + - + -
444A THR* 1.3 71.6 - - - +
446A GLU* 1.3 66.4 + - - +
506A LEU* 5.0 1.8 - - + +
700A ANP 3.1 28.1 + - - -
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Residues in contact with GLU 446 (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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353A ARG* 2.7 48.2 + - + +
354A GLU 3.8 8.3 - - - +
355A VAL* 4.4 2.2 - - - -
419A ARG* 4.2 5.0 + - - -
429A TYR* 5.9 1.4 - - - -
431A PRO* 3.4 15.6 - - + +
432A GLU* 3.0 39.7 + - - +
434A VAL* 4.2 4.2 - - - +
445A THR* 1.3 69.3 - - - +
447A LEU* 1.3 67.2 + - - +
448A VAL* 5.8 0.2 - - + -
700A ANP 2.8 19.5 + - - -
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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