Contacts of the helix formed by residues 516 - 526 (chain A) in PDB entry 2YD0
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 ASP 516 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451A TYR* 4.8 4.1 + - - -
483A ALA* 5.6 1.6 - - - +
514A GLY 4.3 0.8 + - - -
515A VAL* 1.3 73.6 - - - +
517A VAL* 1.3 64.5 + - - +
518A LYS* 3.3 18.2 + - - +
519A THR* 2.7 32.8 + - - -
520A MET* 3.3 20.7 + - - +
564A HIS* 5.0 5.5 + - + +
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Residues in contact with VAL 517 (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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448A LEU* 3.9 15.9 - - + -
451A TYR* 4.8 4.0 - - + -
452A LEU* 4.0 27.8 - - + -
479A TRP* 4.4 6.3 - - + +
482A MET* 4.1 31.0 - - + +
483A ALA* 4.5 16.8 - - + +
515A VAL* 4.0 14.8 + - + -
516A ASP* 1.3 73.8 + - - +
518A LYS* 1.3 52.4 + - - +
520A MET* 3.2 6.1 + - - +
521A MET* 2.7 51.2 + - + +
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Residues in contact with LYS 518 (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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476A GLU* 2.6 36.2 + - + +
479A TRP* 4.1 28.2 - - + +
480A ASP* 3.1 29.7 + - - +
483A ALA* 4.9 11.5 - - + +
516A ASP* 3.3 8.4 + - - +
517A VAL* 1.3 75.7 - - - +
519A THR* 1.3 68.6 + - - +
521A MET* 4.4 0.4 - - - +
522A ASN* 2.9 42.9 + - - +
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Residues in contact with THR 519 (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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516A ASP* 2.7 29.1 + - - -
518A LYS* 1.3 80.3 - - - +
520A MET* 1.3 64.9 + - - +
522A ASN* 3.5 9.4 + - - +
523A THR* 3.3 20.4 + - + +
564A HIS* 3.7 26.0 - - + +
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Residues in contact with MET 520 (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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447A MET* 6.4 0.4 - - - -
448A LEU* 4.7 6.3 - - - -
451A TYR* 4.0 27.4 - - + -
516A ASP 3.3 13.8 + - - +
517A VAL* 3.2 9.1 + - - +
518A LYS 3.1 0.6 - - - -
519A THR* 1.3 79.6 - - - +
521A MET* 1.3 79.5 + - - +
523A THR* 2.7 26.0 + - - -
524A TRP* 3.4 6.2 - - + -
564A HIS* 3.9 36.7 + - + +
566A PRO* 4.6 10.5 - - + -
581A LEU* 3.2 46.7 - - + -
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Residues in contact with MET 521 (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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444A ILE* 4.1 40.6 - - + +
445A LEU* 5.4 1.1 - - + -
447A MET* 5.5 1.6 - - - -
448A LEU* 3.9 25.4 - - + -
479A TRP* 3.5 52.7 - - + -
517A VAL* 2.7 33.6 + - + +
520A MET* 1.3 83.1 - - + +
522A ASN* 1.3 61.3 + - - +
524A TRP* 3.2 14.2 + - + +
525A THR* 2.7 33.9 + - - +
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Residues in contact with ASN 522 (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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475A ASN* 4.1 7.8 + - - -
479A TRP* 3.6 20.3 + - - -
518A LYS* 2.9 35.6 + - - +
519A THR* 3.8 8.9 - - - +
521A MET* 1.3 75.2 - - - +
523A THR* 1.3 65.5 + - + +
525A THR* 3.6 2.9 - - - -
526A LEU* 2.9 47.9 + - + +
527A GLN* 4.3 0.3 + - - +
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Residues in contact with THR 523 (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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519A THR* 3.3 18.2 - - + +
520A MET 2.7 15.9 + - - +
522A ASN* 1.3 76.8 - - + +
524A TRP* 1.3 66.9 + - - +
527A GLN* 3.1 34.2 - - - +
562A LEU 3.7 24.0 - - - +
563A TRP* 3.2 12.6 + - - -
564A HIS* 3.4 32.5 + - + +
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Residues in contact with TRP 524 (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 VAL* 4.0 2.9 - - - +
440A LYS* 3.9 23.6 + - - +
444A ILE* 3.8 33.4 - - + +
447A MET* 3.3 36.1 - - + +
520A MET* 3.4 23.2 + - + +
521A MET* 3.2 23.2 + - + +
522A ASN 3.0 0.6 - - - -
523A THR* 1.3 83.5 + - - +
525A THR* 1.3 58.4 + - - +
527A GLN 4.4 3.2 - - - +
529A GLY 4.7 0.2 - - - -
530A PHE* 4.6 1.8 - - - -
531A PRO* 3.5 21.8 - - + -
563A TRP* 3.4 37.2 - + + +
564A HIS 3.0 24.5 + - - -
565A VAL* 4.3 11.9 - - + -
566A PRO* 4.7 0.8 - - - +
607A TYR* 3.3 40.2 - + + -
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Residues in contact with THR 525 (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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373A TRP* 3.9 14.4 - - + -
418A PRO* 3.6 1.9 - - - +
419A VAL* 3.5 15.8 + - + -
420A SER* 3.1 28.8 + - - +
444A ILE* 3.7 20.6 - - + -
475A ASN* 3.3 26.0 + - - -
479A TRP* 3.7 19.8 + - + -
521A MET 2.7 21.7 + - - +
522A ASN* 3.6 6.6 - - - -
524A TRP* 1.3 84.1 - - - +
526A LEU* 1.3 60.6 + - - +
527A GLN 3.6 2.0 - - - -
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Residues in contact with LEU 526 (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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418A PRO* 3.8 14.6 - - - +
420A SER* 4.3 22.7 - - - +
475A ASN* 4.5 8.1 - - - +
522A ASN* 2.9 38.7 + - + +
525A THR* 1.3 88.1 - - - +
527A GLN* 1.3 60.6 + - - +
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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