Contacts of the helix formed by residues 511 - 520 (chain A) in PDB entry 1XR2
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 THR 511 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465A ARG* 3.3 30.7 - - - +
471A PHE* 3.9 7.0 - - + -
472A PHE* 3.8 23.1 - - + -
510A MET* 1.3 81.4 - - - +
512A LEU* 1.3 65.9 + - - +
513A LYS 3.3 2.5 - - - -
514A GLU* 3.2 13.3 + - - +
515A ILE* 2.9 34.9 + - - +
529A MET 4.5 2.7 + - - +
530A LEU* 4.3 5.6 - - + +
562A GLU* 2.6 28.6 + - - +
566A LEU* 4.1 7.1 - - - +
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Residues in contact with LEU 512 (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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509A PRO* 3.5 34.5 - - + -
510A MET 3.8 1.6 - - - +
511A THR* 1.3 76.7 + - - +
513A LYS* 1.3 57.4 + - - +
515A ILE* 4.6 2.5 - - - +
516A THR* 2.7 43.5 + - - +
562A GLU* 3.8 2.9 + - - +
565A ASP* 3.6 42.2 - - + +
566A LEU* 3.8 20.9 - - + -
569A ALA* 3.9 16.8 - - + -
571A ILE* 4.9 0.2 - - + -
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Residues in contact with LYS 513 (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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440A LYS* 5.8 0.5 - - - +
511A THR 3.3 0.4 + - - -
512A LEU* 1.3 76.5 - - - +
514A GLU* 1.3 72.2 + - - +
516A THR* 4.1 3.5 - - - -
517A TYR* 3.1 27.5 + - - +
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Residues in contact with GLU 514 (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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439A ILE* 6.1 2.9 - - + -
443A ILE* 4.3 17.5 - - + +
460A HIS* 4.0 20.0 - - + +
464A GLU* 3.8 33.8 - - + +
471A PHE* 4.6 6.6 - - - -
475A LYS* 5.3 3.6 + - - -
510A MET 3.8 6.1 - - - +
511A THR* 3.2 26.9 - - - +
513A LYS* 1.3 83.8 - - - +
515A ILE* 1.3 64.1 + - + +
517A TYR* 4.0 2.9 - - - +
518A ALA* 3.2 23.0 + - - +
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Residues in contact with ILE 515 (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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460A HIS* 3.6 33.9 - - + +
465A ARG* 4.5 0.4 - - - +
511A THR* 2.9 34.9 + - - +
512A LEU 3.8 1.6 - - - +
514A GLU* 1.3 72.2 - - + +
516A THR* 1.3 65.9 + - - +
518A ALA* 3.2 7.0 + - - +
519A GLN* 3.0 21.6 + - + +
526A VAL* 4.6 8.6 - - + +
527A LYS 4.2 5.4 - - - +
528A GLY* 4.1 24.0 - - - -
529A MET 4.2 3.6 - - - +
566A LEU* 3.9 14.6 - - + -
571A ILE* 3.4 31.4 - - + -
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Residues in contact with THR 516 (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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512A LEU* 2.7 42.5 + - - +
513A LYS* 4.1 3.8 - - - -
515A ILE* 1.3 73.6 - - - +
517A TYR* 1.3 64.3 + - - +
519A GLN* 3.2 7.4 + - - +
520A SER* 3.1 24.0 + - - -
569A ALA* 4.2 15.0 - - + +
571A ILE* 4.8 4.6 - - - +
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Residues in contact with TYR 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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440A LYS* 3.4 75.2 + - + +
443A ILE* 4.2 13.2 - - + -
444A LYS* 4.0 6.1 - - - +
513A LYS 3.1 18.1 + - - +
514A GLU* 4.0 3.1 - - - +
516A THR* 1.3 80.3 - - - +
518A ALA* 1.3 62.4 + - - +
520A SER* 2.8 25.9 + - - -
521A LEU* 3.4 45.9 - - + +
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Residues in contact with ALA 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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443A ILE* 3.8 16.6 - - + -
447A ILE* 4.0 10.2 - - + +
460A HIS* 3.7 24.9 - - + -
514A GLU 3.2 14.2 + - - +
515A ILE 3.4 9.0 - - - +
516A THR 3.2 0.2 - - - -
517A TYR* 1.3 79.5 - - - +
519A GLN* 1.3 61.2 + - - +
521A LEU* 3.3 18.9 + - - +
522A THR* 3.8 10.7 - - - +
526A VAL* 4.1 13.5 - - + -
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Residues in contact with GLN 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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515A ILE 3.0 15.7 + - - +
516A THR* 3.2 8.0 + - - +
518A ALA* 1.3 72.5 - - - +
520A SER* 1.3 55.5 + - - +
521A LEU 3.1 4.9 - - - -
522A THR* 2.9 35.1 + - - +
523A GLU 4.5 2.6 + - - -
524A LYS 2.7 26.6 + - - +
525A PRO* 3.8 3.3 - - - +
526A VAL* 3.0 37.2 + - + +
570A GLY 4.9 13.8 - - - +
571A ILE* 5.1 12.0 - - + -
572A LYS* 5.4 8.3 + - - +
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Residues in contact with SER 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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516A THR* 3.1 13.5 + - - -
517A TYR* 2.8 30.7 + - - -
518A ALA 3.3 0.2 - - - -
519A GLN* 1.3 75.6 - - - +
521A LEU* 1.3 64.4 + - - +
522A THR 3.4 1.1 + - - -
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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