Contacts of the strand formed by residues 357 - 361 (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 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A TYR* 3.3 12.4 + - + +
356A VAL* 1.3 71.2 - - - +
358A THR* 1.3 65.0 + - - +
369A ASP* 3.0 31.7 + - - -
370A ASN 4.0 0.2 - - - -
371A VAL* 3.5 35.5 - - + +
404A LEU* 3.1 8.8 - - - +
405A SER* 2.9 35.5 + - - +
406A ILE 5.9 0.4 - - - +
407A CYS 5.9 1.3 - - - +
455A LEU 5.6 6.2 + - - -
456A LEU* 3.7 30.2 - - + +
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Residues in contact with THR 358 (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* 4.0 17.3 - - + -
356A VAL* 4.0 11.7 - - + +
357A ARG* 1.3 79.2 - - - +
359A GLY* 1.3 58.2 + - - +
369A ASP* 3.1 6.8 - - - +
370A ASN 2.5 53.6 + - - +
387A LEU* 3.3 17.4 - - + +
389A TYR* 2.9 34.9 + - - +
402A LEU* 4.2 8.1 - - + -
403A CYS 3.3 4.3 - - - -
404A LEU* 4.1 8.5 - - + -
456A LEU* 4.4 4.5 - - - -
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Residues in contact with GLY 359 (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* 1.3 75.4 - - - +
360A ILE* 1.3 65.7 + - - -
361A TYR* 3.9 14.1 - - - -
369A ASP* 3.4 16.2 - - - -
389A TYR* 4.9 0.2 - - - -
402A LEU* 3.4 9.4 - - - +
403A CYS 2.6 40.3 + - - -
456A LEU* 4.1 1.5 - - - +
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Residues in contact with ILE 360 (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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334A LEU* 3.8 20.0 - - + -
336A ILE* 4.1 7.4 - - + -
359A GLY* 1.3 75.5 - - - +
361A TYR* 1.3 64.5 + - - +
365A GLU* 4.3 0.3 - - - -
366A PRO* 2.9 44.9 - - + +
367A LEU* 4.2 16.9 - - + +
369A ASP* 4.6 0.5 - - - +
389A TYR* 3.4 49.4 - - + -
391A ILE* 4.4 7.2 - - + -
396A LEU* 4.1 22.2 - - + -
400A ALA* 4.7 4.5 - - + -
401A ARG 3.3 2.9 - - - +
402A LEU* 4.9 1.3 - - + -
429A LEU* 4.1 14.8 - - + -
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Residues in contact with TYR 361 (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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359A GLY* 3.9 10.3 - - - -
360A ILE* 1.3 81.4 - - - +
362A HIS* 1.3 58.7 + - - +
363A GLY 3.8 14.1 - - - -
364A GLY* 4.0 4.3 - - - -
365A GLU* 3.0 45.0 + - + +
366A PRO* 3.5 3.8 - - - -
369A ASP* 3.9 15.0 + - + -
399A ALA 3.9 0.5 - - - +
400A ALA* 3.3 5.3 - - - -
401A ARG* 2.6 50.3 + - - +
403A CYS* 3.6 34.1 - - + -
456A LEU* 3.7 27.2 - - + +
458A PRO* 3.6 23.4 - - + +
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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