Contacts of the helix formed by residues 505 - 514 (chain J) in PDB entry 6XAV
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 505 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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806I PRO* 5.6 8.5 - - + -
809I GLY* 4.1 6.9 - - - -
812I PHE* 3.0 42.6 - - - +
1099I ASN* 6.2 1.1 - - - +
1101I LEU* 5.9 0.4 - - + -
503J SER 2.9 13.0 - - - +
504J GLN* 1.3 80.4 - - - +
506J VAL* 1.3 66.2 + - - +
507J VAL 3.7 0.7 - - - -
508J LEU* 4.2 8.9 - - - +
509J GLY 3.5 9.9 + - - -
628J GLY 3.3 17.5 - - - +
629J PHE* 3.1 27.2 - - + -
632J ALA* 3.7 11.6 - - + +
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Residues in contact with VAL 506 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812I PHE* 5.7 0.9 - - + -
452J LEU* 5.6 0.2 - - + -
502J PRO* 3.7 32.3 - - + -
503J SER 4.3 1.0 + - - -
505J ASP* 1.3 79.0 + - - +
507J VAL* 1.3 62.5 + - + +
508J LEU 3.3 1.6 - - - -
510J LEU* 3.0 41.8 + - + +
601J ILE* 4.2 3.1 - - + +
624J ILE* 3.5 41.5 - - + +
625J MET* 4.1 13.7 - - + +
628J GLY* 4.1 4.7 - - - -
629J PHE* 3.7 28.5 - - + -
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Residues in contact with VAL 507 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502J PRO* 3.4 22.0 - - + +
503J SER* 3.9 2.9 - - - +
504J GLN 3.6 25.4 - - - +
506J VAL* 1.3 78.1 - - + +
508J LEU* 1.3 59.7 + - - +
511J TYR* 3.2 25.2 + - - +
596J LEU 4.4 4.2 - - - +
598J LYS* 4.1 21.1 - - + +
601J ILE* 3.6 29.4 - - + -
728J SER* 3.8 14.8 - - - +
729J GLY 4.5 3.8 - - - +
730J ALA* 3.6 23.6 - - - +
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Residues in contact with LEU 508 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806I PRO* 5.9 3.6 - - + -
1101I LEU* 3.8 35.0 - - + -
504J GLN 5.1 0.7 - - - +
505J ASP* 4.6 9.2 - - - +
506J VAL 3.3 1.4 - - - +
507J VAL* 1.3 82.0 - - - +
509J GLY* 1.3 64.1 + - - +
511J TYR* 3.3 7.2 + - + +
512J TYR* 3.0 22.9 + - + +
632J ALA* 5.8 6.3 - - + -
635J SER* 6.1 0.7 - - - +
637J ALA* 4.6 18.4 - - + -
724J MET* 4.1 32.1 - - + +
725J MET* 4.4 9.6 - - + +
728J SER* 3.8 17.9 - - - +
730J ALA* 4.3 11.0 - - + -
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Residues in contact with GLY 509 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505J ASP 3.5 12.7 + - - -
506J VAL 3.5 4.1 + - - -
508J LEU* 1.3 79.6 - - - +
510J LEU* 1.3 62.5 + - - +
512J TYR* 3.1 15.9 + - - +
513J MET* 3.2 20.1 + - - +
628J GLY* 4.3 6.7 - - - -
631J TYR* 4.6 3.4 - - - +
632J ALA* 4.2 21.5 - - - +
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Residues in contact with LEU 510 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506J VAL* 3.0 37.9 + - + +
509J GLY* 1.3 76.3 - - - +
511J TYR* 1.3 52.2 + - - +
513J MET* 3.7 26.0 - - + -
514J THR* 2.6 42.3 + - - +
579J LEU* 4.1 22.4 - - + -
595J ALA 4.6 0.9 - - - -
596J LEU* 4.7 9.0 - - + +
601J ILE* 3.7 29.8 - - + -
604J MET* 4.9 6.5 - - + -
624J ILE* 4.0 23.1 - - + +
627J THR* 4.2 4.3 - - + -
628J GLY* 3.9 13.9 - - - -
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Residues in contact with TYR 511 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507J VAL 3.2 20.9 + - - +
508J LEU* 3.3 8.9 + - + +
509J GLY 3.2 0.4 - - - -
510J LEU* 1.3 79.5 - - - +
512J TYR* 1.3 57.7 + - + +
514J THR* 3.5 5.6 + - - -
515J ARG* 3.2 67.9 + - - +
595J ALA* 3.8 32.3 - - + +
596J LEU 4.4 2.6 + - - +
597J GLY* 4.9 4.7 - - - -
717J VAL* 4.4 4.7 - - - +
723J TYR* 4.8 1.9 - - - -
724J MET* 4.0 26.0 - - + -
727J ASP* 3.8 28.0 + - + +
728J SER* 3.6 26.5 - - - -
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Residues in contact with TYR 512 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1222I GLU* 4.2 26.4 + - - +
1223I ARG* 5.0 18.9 - - + +
508J LEU* 3.0 14.6 + - + +
509J GLY* 3.1 11.4 + - - +
511J TYR* 1.3 77.7 - - + +
513J MET* 1.3 64.8 + - + +
515J ARG* 3.5 16.5 - - + +
537J TYR* 5.3 3.6 - - - -
544J LEU* 3.6 32.1 - - + +
545J HIS* 4.0 30.1 + + - -
631J TYR 4.8 5.2 - - - +
635J SER* 3.8 37.2 - - - +
637J ALA* 6.5 0.4 - - + -
719J PHE* 5.4 5.8 - + - -
724J MET* 4.9 17.7 - - + -
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Residues in contact with MET 513 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509J GLY 3.2 10.1 + - - +
510J LEU* 3.7 38.1 - - + +
512J TYR* 1.3 74.7 - - + +
514J THR* 1.3 58.5 + - + +
515J ARG 3.1 16.4 + - - +
544J LEU* 3.7 27.2 - - + +
573J THR* 4.1 0.2 + - - -
575J GLY* 3.2 36.6 + - - +
576J ARG 3.8 1.0 + - - -
578J ILE* 5.9 2.2 - - - -
579J LEU* 3.8 26.7 - - + -
627J THR* 3.8 10.5 - - - +
631J TYR* 3.4 42.8 - - + -
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Residues in contact with THR 514 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510J LEU 2.6 22.2 + - - +
511J TYR* 3.5 3.3 - - - -
513J MET* 1.3 70.6 - - + +
515J ARG* 1.3 62.0 + - - +
516J ASP* 4.3 0.2 - - - +
576J ARG* 2.8 48.3 + - + -
579J LEU* 4.1 14.1 - - + -
592J VAL 4.4 2.2 - - - +
594J GLN 3.3 17.1 - - - +
595J ALA* 2.4 28.9 + - - -
596J LEU* 3.6 29.2 - - + -
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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