Contacts of the strand formed by residues 442 - 446 (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 GLY 442 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414A GLU* 3.3 16.8 - - - -
415A VAL 3.1 5.5 + - - +
416A MET* 3.4 8.3 - - - -
417A LEU* 3.0 23.2 + - - +
440A LEU* 4.4 2.1 - - - +
441A THR* 1.3 81.1 + - - +
443A ILE* 1.3 67.6 + - - +
466A ILE* 3.7 2.5 - - - +
467A PRO 3.4 9.4 - - - -
469A ARG* 3.8 4.5 - - - -
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Residues in contact with ILE 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A MET* 3.8 3.3 - - - -
417A LEU* 3.5 23.6 - - + +
419A ILE* 4.0 20.6 - - + -
431A ALA* 4.8 5.8 - - + -
440A LEU* 4.6 2.2 - - + -
442A GLY* 1.3 79.6 - - - +
444A THR* 1.3 75.3 + - - +
445A LEU* 4.4 4.5 - - + +
460A VAL* 3.6 29.6 - - + -
464A PHE* 5.2 2.0 - - + -
466A ILE* 3.9 36.6 - - + +
467A PRO 2.9 10.6 + - - +
468A ILE* 3.4 13.3 - - + +
469A ARG* 2.8 30.1 + - - +
470A TYR 3.6 1.7 + - - -
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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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309A THR* 3.9 24.7 - - + +
416A MET* 3.3 20.0 - - - +
417A LEU 2.7 14.6 + - - +
418A THR* 3.3 9.5 - - + -
419A ILE* 3.0 28.6 + - - +
443A ILE* 1.3 74.3 - - - +
445A LEU* 1.3 60.8 + - - +
446A THR* 4.1 8.7 - - + -
470A TYR* 3.5 24.1 - - - +
480A LEU* 3.8 28.3 - - + -
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Residues in contact with LEU 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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419A ILE* 3.3 29.4 - - + +
420A ASP 4.1 0.4 - - - -
421A ALA* 3.5 40.2 - - + +
443A ILE* 4.1 5.6 - - + -
444A THR* 1.3 72.3 - - - +
446A THR* 1.3 59.5 + - - +
448A LEU* 3.1 19.7 - - + +
456A VAL* 4.0 8.1 - - + -
457A ILE* 3.7 44.9 - - + +
460A VAL* 5.6 1.8 - - + -
468A ILE* 4.9 7.0 - - + -
470A TYR 3.1 11.3 + - - +
471A ILE* 3.3 6.0 - - + -
472A GLY 2.8 23.0 + - - -
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Residues in contact with THR 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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304A VAL 2.9 21.8 + - - +
305A GLY* 4.4 6.0 - - - +
309A THR* 3.7 23.1 - - - +
418A THR* 3.7 17.0 - - + -
419A ILE 2.8 14.4 + - - -
420A ASP* 3.4 9.2 - - - +
421A ALA* 2.8 27.5 + - - +
444A THR* 4.1 7.0 - - + -
445A LEU* 1.3 74.1 - - - +
447A LYS* 1.3 74.1 + - - +
448A LEU 3.2 3.3 + - - -
472A GLY* 4.1 5.6 - - - +
480A LEU* 5.3 4.3 - - + -
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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