Contacts of the strand formed by residues 468 - 472 (chain A) in PDB entry 2YHS
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 ILE 468 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A VAL* 2.9 30.5 + - + +
284A GLU 4.7 5.0 + - - +
443A ILE* 3.4 18.8 - - + +
445A LEU* 4.9 9.0 - - + -
457A ILE* 3.6 37.7 - - + +
460A VAL* 4.3 15.9 - - + -
461A ALA* 4.5 2.0 - - + -
466A ILE 4.0 4.7 - - - +
467A PRO* 1.3 70.8 - - - +
469A ARG* 1.3 59.7 + - - +
470A TYR 3.8 17.5 - - - +
471A ILE* 4.0 9.4 - - + -
483A PHE* 3.2 46.9 - - + +
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Residues in contact with ARG 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU* 2.7 64.8 + - - +
285A PRO* 3.9 10.9 + - - +
286A LEU* 3.8 21.6 + - + +
414A GLU* 2.9 43.7 + - - +
416A MET* 3.8 10.8 - - + -
441A THR* 3.2 20.9 + - - -
442A GLY* 3.8 9.6 - - - -
443A ILE 2.8 12.5 + - - +
467A PRO* 3.6 11.5 - - - +
468A ILE* 1.3 72.8 - - - +
470A TYR* 1.3 84.3 + - + +
482A PRO* 3.4 4.7 - - - +
483A PHE 2.9 18.6 + - - +
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Residues in contact with TYR 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 3.9 30.5 + - + +
313A LEU* 3.5 24.4 - - + +
316A GLN* 3.8 18.6 + - - -
317A PHE* 3.8 17.7 - - - -
320A GLN* 5.9 0.5 + - - -
416A MET* 4.1 4.7 - - + -
443A ILE 3.6 2.2 + - - -
444A THR* 3.5 17.3 - - - +
445A LEU 3.1 23.8 + - - -
468A ILE* 3.5 3.2 - - - +
469A ARG* 1.3 96.6 - - + +
471A ILE* 1.3 68.5 + - - +
480A LEU* 3.7 29.8 - - + -
481A ARG 3.2 8.3 - - - +
482A PRO* 3.7 33.9 - - + -
483A PHE* 4.0 1.3 - - - +
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Residues in contact with ILE 471 (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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199A LEU* 5.1 1.3 - - + -
445A LEU* 3.3 7.4 - - + +
448A LEU* 3.9 16.2 - - + -
457A ILE* 4.0 13.0 - - + -
468A ILE* 4.0 10.3 - - + -
470A TYR* 1.3 80.3 - - - +
472A GLY* 1.3 60.6 + - - +
473A VAL* 3.6 15.2 + - + -
479A ASP 3.3 2.8 - - - +
480A LEU* 4.0 3.1 - - - -
481A ARG* 2.9 43.4 + - + +
483A PHE* 3.8 22.0 - - + -
488A PHE* 3.7 26.7 - - + -
1499A EDO 3.6 29.6 - - - +
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Residues in contact with GLY 472 (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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312A LYS* 5.8 1.1 - - - -
445A LEU 2.8 15.0 + - - -
446A THR* 4.3 3.4 - - - -
447A LYS 3.4 10.6 + - - -
448A LEU* 2.9 29.3 + - - +
449A ASP* 3.8 0.8 - - - +
471A ILE* 1.3 71.3 - - - +
473A VAL* 1.3 62.9 + - - +
474A GLY 3.6 5.4 - - - -
479A ASP 3.6 4.9 - - - -
480A LEU* 4.0 13.7 - - - +
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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