Contacts of the strand formed by residues 401 - 405 (chain A) in PDB entry 2RD0
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 401 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A ILE* 3.3 4.3 - - - -
361A TYR* 2.6 52.3 + - + +
362A HIS* 4.7 0.4 - - - +
363A GLY* 3.7 29.7 + - - +
399A ALA 3.7 15.7 + - - +
400A ALA* 1.3 75.1 - - - +
402A LEU* 1.3 65.5 + - - +
403A CYS* 3.4 4.5 + - - -
426A ASN* 3.3 15.4 - - - +
427A ILE 3.2 15.0 - - - +
428A ASN* 3.6 21.1 - - - +
429A LEU* 4.0 4.3 - - - -
458A PRO* 2.6 38.2 + - - +
460A GLY 4.5 2.2 + - - -
463A GLY* 4.5 13.0 - - - -
607A PRO* 5.5 7.0 - - - +
643A GLN* 3.9 9.9 - - - +
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Residues in contact with LEU 402 (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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336A ILE* 4.0 27.1 - - + -
338A ILE* 5.5 0.4 - - + -
358A THR* 4.2 20.6 - - + -
359A GLY 3.4 15.7 - - - +
360A ILE* 4.8 2.0 - - + +
389A TYR* 4.4 0.7 - - - +
401A ARG* 1.3 68.8 - - - +
403A CYS* 1.3 69.4 + - - +
404A LEU* 4.0 22.6 + - + -
425A GLY 4.1 0.2 - - - +
426A ASN* 3.2 5.4 - - - +
427A ILE* 2.8 47.3 + - + +
429A LEU* 3.6 21.8 - - + +
475A LEU* 4.2 11.9 - - + -
477A PHE* 4.0 23.8 - - + -
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Residues in contact with CYS 403 (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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358A THR* 3.3 2.9 - - - -
359A GLY 2.6 39.7 + - - +
361A TYR* 3.6 41.7 - - + -
401A ARG* 3.4 8.7 + - - -
402A LEU* 1.3 76.7 - - - +
404A LEU* 1.3 59.2 + - - +
426A ASN* 3.3 32.5 - - - +
456A LEU* 3.8 16.3 - - + +
457A ASN 4.9 0.9 - - - +
458A PRO* 3.8 14.4 - - + -
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Residues in contact with LEU 404 (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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338A ILE* 5.0 0.2 - - + -
356A VAL* 4.0 18.4 - - + -
357A ARG 3.1 13.0 - - - +
358A THR* 4.1 7.4 - - + -
402A LEU* 4.0 26.7 - - + +
403A CYS* 1.3 75.3 - - - +
405A SER* 1.3 65.4 + - - +
424A TRP* 3.7 5.7 - - - -
425A GLY* 2.8 42.1 + - - +
426A ASN* 3.9 0.2 + - - -
443A LEU* 4.5 7.2 - - + -
445A LEU* 3.6 35.9 - - + -
456A LEU* 3.4 6.1 - - - +
473A LEU* 4.8 7.9 - - + -
475A LEU* 4.4 22.0 - - + -
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Residues in contact with SER 405 (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 VAL* 3.3 7.4 - - - +
357A ARG* 2.9 33.9 + - - +
404A LEU* 1.3 79.0 - - - +
406A ILE* 1.3 65.8 + - - +
407A CYS* 4.7 9.4 + - - +
424A TRP* 3.8 26.5 - - - +
448A VAL* 6.1 0.2 - - - -
455A LEU 4.6 2.6 + - - -
456A LEU* 3.2 28.7 - - - +
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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