Contacts of the strand formed by residues 469 - 471 (chain A) in PDB entry 6A5T
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 PHE 469 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ALA* 4.9 2.7 - - + -
351A ARG 4.6 4.0 - - - -
352A THR* 3.3 29.6 - - + -
353A VAL 3.0 6.1 + - - -
354A ILE* 3.6 20.1 - - + +
355A SER* 2.3 44.2 + - - +
365A VAL* 5.1 0.9 - - + -
366A GLY 3.4 9.4 - - - -
367A VAL* 4.7 4.0 - - + -
368A PRO* 3.8 15.0 - - + -
371A ILE* 4.0 15.9 - - + -
445A PHE* 3.6 23.6 - + + -
468A THR* 1.3 84.5 - - - +
470A ARG* 1.3 56.3 + - - +
471A LEU* 4.6 4.9 - - + -
488A MET 3.8 8.7 - - - -
490A LEU* 3.5 46.9 - - + -
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Residues in contact with ARG 470 (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 SER* 3.2 6.3 - - - +
357A ASP* 3.9 19.2 + - + +
360A LEU* 4.3 11.9 - - + -
365A VAL* 3.2 14.2 - - - +
366A GLY* 2.6 48.6 + - - +
368A PRO* 4.5 0.6 - - - +
464A MET* 3.7 34.8 + - - +
465A PRO 2.3 28.5 + - - -
466A TYR* 2.8 30.2 + - - +
468A THR* 3.1 25.2 + - - +
469A PHE* 1.3 74.8 - - - +
471A LEU* 1.3 61.8 + - - +
976B ILE* 4.1 6.7 - - - +
67K LEU* 3.4 29.1 - - - +
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Residues in contact with LEU 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ILE* 4.1 33.0 - - + -
355A SER 2.9 10.4 + - - +
356A GLY* 4.8 4.0 - - - -
357A ASP* 3.1 22.0 + - - +
360A LEU* 3.2 15.8 - - - +
364A GLN 4.7 4.3 - - - -
365A VAL* 5.1 1.8 - - + +
445A PHE* 3.8 30.5 - - + -
459A HIS* 5.7 5.4 - - + +
469A PHE* 4.4 1.6 - - + +
470A ARG* 1.3 79.0 - - - +
472A ASN* 1.3 68.7 + - - +
475A VAL* 3.9 27.6 - - + +
476A THR* 5.1 3.4 - - + -
479A TYR* 5.4 7.0 - - + -
481A ALA* 5.7 2.5 - - + +
483A PHE* 4.6 11.0 - - + -
488A MET* 5.0 4.7 - - - -
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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