Contacts of the helix formed by residues 507 - 516 (chain A) in PDB entry 2XR9
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 GLU 507 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503A PHE* 4.5 3.1 - - + -
504A GLU* 3.5 24.5 - - + +
505A ASN 3.0 1.6 - - - -
506A ILE* 1.3 88.3 - - + +
508A LEU* 1.3 62.8 + - - +
509A TYR 3.5 0.8 + - - -
510A ASN* 3.6 15.2 + - - +
511A VAL* 3.8 13.2 + - - +
525A GLY* 3.4 6.7 - - - -
526A THR 2.8 34.5 + - - +
529A SER* 3.2 21.0 + - - +
530A LEU* 3.6 25.6 - - + +
825A ARG* 4.0 9.9 + - - -
853A THR* 3.9 19.5 - - + +
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Residues in contact with LEU 508 (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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201A MET* 3.5 30.7 - - - -
216A LEU* 3.8 30.5 - - + -
354A ILE* 5.0 9.2 - - + -
356A VAL* 4.4 5.8 - - + -
487A PHE* 3.8 32.5 - - + -
503A PHE* 3.9 18.4 - - + -
505A ASN 3.3 5.9 + - - +
507A GLU* 1.3 76.7 - - - +
509A TYR* 1.3 60.8 + - - +
511A VAL* 3.0 15.0 + - + +
512A MET* 2.8 36.8 + - + +
530A LEU* 4.1 9.9 - - + -
533A LEU* 4.8 1.6 - - + -
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Residues in contact with TYR 509 (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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216A LEU 3.9 7.6 + - - +
217A ALA 3.2 26.5 - - - -
218A THR 3.6 13.9 - - - -
219A GLY* 3.4 22.2 - - - +
257A GLN 3.7 10.2 + - - -
259A LEU* 3.9 14.8 - - + -
262A THR* 2.6 31.3 + - - +
505A ASN 4.7 1.2 + - - -
506A ILE 4.4 1.2 + - - -
507A GLU 3.5 1.2 - - - -
508A LEU* 1.3 76.5 - - - +
510A ASN* 1.3 63.5 + - - +
512A MET* 3.3 10.9 + - + +
513A CYS* 3.0 36.5 + - - -
520A PRO* 3.6 20.4 - - + -
521A ALA* 2.9 28.3 + - + +
523A ASN* 3.6 22.9 - - + -
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Residues in contact with ASN 510 (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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506A ILE 5.2 0.2 + - - -
507A GLU* 3.6 10.7 + - - +
508A LEU 3.3 0.6 - - - -
509A TYR* 1.3 79.3 - - - +
511A VAL* 1.3 59.9 + - + +
513A CYS* 3.4 6.4 + - - +
514A ASP* 2.9 33.8 + - - +
520A PRO* 3.4 14.9 - - - +
523A ASN* 2.9 37.2 + - - +
525A GLY* 3.8 13.5 + - - -
526A THR 4.0 1.0 + - - +
527A HIS* 3.6 52.3 + - + +
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Residues in contact with VAL 511 (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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354A ILE* 5.5 0.7 - - + -
494A PHE* 4.8 8.1 - - + -
507A GLU 3.8 6.1 - - - +
508A LEU* 3.0 17.7 + - + +
510A ASN* 1.3 76.2 - - + +
512A MET* 1.3 61.8 + - + +
514A ASP* 3.2 11.9 + - - +
515A LEU* 2.8 41.3 + - + +
527A HIS* 6.4 0.2 - - + -
530A LEU* 3.6 47.1 - - + +
533A LEU* 5.0 3.4 - - + -
534A LEU* 4.1 25.4 - - + -
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Residues in contact with MET 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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165A LEU* 4.1 4.9 - - + -
167A ILE* 3.8 34.8 - - + -
216A LEU* 3.2 42.2 - - + +
217A ALA* 4.9 3.6 - - - -
259A LEU* 3.9 23.8 - - + -
354A ILE* 4.0 24.7 - - + -
508A LEU* 2.8 30.0 + - + +
509A TYR* 3.8 9.2 - - + +
511A VAL* 1.3 69.1 - - + +
513A CYS* 1.3 63.3 - - - +
515A LEU* 3.2 9.7 + - - +
516A LEU* 3.2 31.2 + - - +
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Residues in contact with CYS 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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259A LEU* 3.9 10.5 - - - -
262A THR* 4.2 9.2 - - - -
509A TYR* 3.0 38.3 + - - +
510A ASN 3.4 9.9 - - - +
512A MET* 1.3 73.4 - - - +
514A ASP* 1.3 66.9 + - - +
516A LEU* 3.0 2.6 + - - -
517A GLY 2.9 5.0 + - - -
518A LEU* 2.9 48.7 + - - +
520A PRO* 3.8 30.3 - - + -
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Residues in contact with ASP 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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493A THR* 6.0 0.6 - - - +
510A ASN 2.9 17.4 + - - +
511A VAL* 3.4 15.7 - - - +
513A CYS* 1.3 75.4 - - - +
515A LEU* 1.3 62.3 + - - +
516A LEU 3.1 1.2 + - - -
517A GLY* 3.2 10.1 + - - +
518A LEU 4.8 6.1 - - - +
527A HIS* 3.1 36.1 + - - -
531A ASN* 4.7 5.4 - - - +
534A LEU* 4.6 20.4 - - + +
537A ASN* 5.3 0.2 - - - +
538A THR* 3.2 38.2 + - + +
539A PHE* 4.0 7.3 - - - +
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Residues in contact with LEU 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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162A ARG* 5.6 1.0 - - - +
163A PRO* 4.2 15.1 - - - +
165A LEU* 3.8 31.5 - - + +
352A ASN* 3.9 16.9 + - + +
354A ILE* 3.9 8.7 - - + -
493A THR* 3.6 40.5 + - + -
494A PHE* 3.9 23.8 - - + -
511A VAL* 2.8 29.5 + - + +
512A MET* 3.6 10.3 - - - +
513A CYS 3.1 0.4 - - - -
514A ASP* 1.3 74.7 - - - +
516A LEU* 1.3 62.7 + - - +
534A LEU* 4.2 15.0 - - + -
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Residues in contact with LEU 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ARG* 3.8 28.8 + - - +
163A PRO 4.5 3.1 - - - +
165A LEU* 3.9 25.8 - - + +
259A LEU* 4.4 9.6 - - + -
263A ALA* 5.3 0.9 - - + -
268A VAL* 4.3 10.6 - - + +
301A SER* 3.8 34.1 - - - +
302A VAL* 3.9 26.7 - - + -
512A MET 3.2 16.4 + - - +
513A CYS 3.0 4.5 + - - +
515A LEU* 1.3 80.8 - - - +
517A GLY* 1.3 62.4 + - - +
518A LEU* 3.4 26.6 + - + +
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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