Contacts of the helix formed by residues 513 - 528 (chain A) in PDB entry 2XT6
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 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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486A LEU* 3.9 6.1 - - - +
511A ALA 3.1 1.8 + - - -
512A GLU* 1.3 71.5 - - - +
514A VAL* 1.3 64.7 + - - +
515A ILE 3.1 2.8 + - - -
516A PRO* 3.2 10.9 - - + +
517A MET* 3.0 19.9 + - - +
711A GLY 2.7 26.0 + - - +
714A PRO* 3.7 22.2 - - + +
717A CYS* 3.5 38.4 - - + -
739A MET* 4.2 7.4 - - - -
770A SER* 3.8 15.7 - - - -
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Residues in contact with VAL 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A LEU* 3.7 29.6 - - + -
511A ALA 3.1 19.3 + - - +
513A THR* 1.3 76.5 - - - +
515A ILE* 1.4 59.1 + - + +
517A MET* 3.3 3.4 + - - +
518A MET* 2.8 58.8 + - + +
545A VAL* 5.8 1.6 - - + -
642A LEU* 4.0 9.0 - - + -
674A ILE* 4.2 16.2 - - + -
676A VAL* 3.9 25.1 - - + -
739A MET* 3.7 13.6 - - - -
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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
----------------------------------------------------------
485A LYS* 4.1 20.2 - - + +
489A ALA* 3.9 12.3 - - + -
508A LEU* 4.0 14.6 - - + -
512A GLU 3.3 5.6 + - - +
513A THR 3.1 1.4 - - - -
514A VAL* 1.4 75.8 - - + +
516A PRO* 1.4 72.9 - - + +
518A MET* 3.2 0.8 + - - -
519A ASP* 2.9 19.3 + - - +
544A ASN* 3.7 34.3 - - + +
545A VAL* 3.8 31.2 - - + -
548A ASN* 3.8 23.1 - - + +
549A ILE* 3.5 20.3 - - + +
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Residues in contact with PRO 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ILE* 4.0 27.6 - - + +
485A LYS* 4.1 21.5 - - + -
486A LEU* 4.1 18.4 - - + -
512A GLU 3.3 13.7 - - - +
513A THR* 3.2 27.6 - - + +
515A ILE* 1.4 86.3 - - + +
517A MET* 1.4 53.5 + - - +
519A ASP* 3.3 10.2 + - + +
520A ALA* 3.0 28.1 + - - +
714A PRO* 4.5 4.9 - - + +
718A ALA* 4.7 5.0 - - + +
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Residues in contact with MET 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A THR* 3.0 14.5 + - - +
514A VAL* 3.4 9.6 - - - +
516A PRO* 1.4 75.2 - - - +
518A MET* 1.3 57.5 + - - +
520A ALA* 3.2 4.2 + - - -
521A VAL* 3.1 23.1 + - - +
674A ILE* 3.8 36.8 - - + -
709A VAL* 3.6 24.5 - - + -
717A CYS* 3.3 50.5 - - + +
718A ALA* 5.3 0.6 - - - +
721A ALA* 3.3 19.1 - - + +
737A ILE* 3.8 15.7 - - + -
739A MET* 3.7 16.6 - - + +
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Residues in contact with MET 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A VAL* 2.8 30.5 + - + +
515A ILE* 3.7 3.6 - - - +
517A MET* 1.3 69.8 - - - +
519A ASP* 1.3 63.3 + - - +
521A VAL* 3.5 8.7 + - - +
522A ILE* 3.2 29.3 + - - +
535A ILE* 3.8 28.7 - - + -
545A VAL* 3.7 41.7 - - + -
549A ILE* 4.0 15.0 - - + -
640A LEU* 4.2 11.4 - - + -
642A LEU* 3.7 26.2 - - + -
674A ILE* 3.8 19.5 - - + -
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Residues in contact with ASP 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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481A TYR* 3.0 39.9 + - - -
485A LYS* 3.5 26.5 + - + +
515A ILE 2.9 13.1 + - - +
516A PRO* 3.4 10.7 - - + +
517A MET 3.2 0.2 - - - -
518A MET* 1.3 76.8 - - - +
520A ALA* 1.4 52.8 + - - +
522A ILE* 3.4 5.1 + - - +
523A ASP* 2.8 37.2 + - - +
548A ASN 4.7 0.2 - - - +
549A ILE* 3.7 12.0 - - + +
586A TYR* 3.2 26.2 + - - -
722A ARG* 5.7 0.3 + - - -
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Residues in contact with ALA 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A PRO 3.0 12.9 + - - +
517A MET 3.2 9.6 + - - +
519A ASP* 1.4 74.9 + - - +
521A VAL* 1.4 56.2 + - - +
523A ASP* 3.8 1.1 - - - +
524A GLN* 2.9 32.4 + - - +
718A ALA* 3.6 29.8 - - + +
721A ALA* 3.8 3.6 - - + -
722A ARG* 3.5 32.3 - - + +
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Residues in contact with VAL 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A MET 3.1 15.9 + - - +
518A MET* 3.6 8.5 - - - +
520A ALA* 1.4 75.0 - - - +
522A ILE* 1.3 57.7 + - + +
524A GLN 3.2 2.1 + - - -
525A CYS* 3.0 39.5 + - - -
533A VAL* 5.3 1.6 - - + -
638A VAL* 5.7 0.9 - - + -
640A LEU* 4.0 26.7 - - + -
672A ILE* 4.4 15.9 - - + -
674A ILE* 4.2 20.9 - - + -
721A ALA* 3.5 22.6 - - + +
725A VAL* 3.4 22.5 - - + +
737A ILE* 5.0 0.4 - - + -
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Residues in contact with ILE 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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518A MET 3.2 19.3 + - - +
519A ASP* 3.9 3.6 - - - +
521A VAL* 1.3 71.0 - - - +
523A ASP* 1.4 63.7 - - - +
525A CYS* 3.4 8.3 + - - +
526A ALA* 3.1 22.2 + - - +
533A VAL* 4.0 23.3 - - + -
535A ILE* 4.1 13.5 - - + -
549A ILE* 3.4 32.3 - - + +
586A TYR* 3.5 33.7 - - + -
595A ILE* 3.6 14.7 - - + +
597A VAL* 3.8 14.8 - - + -
640A LEU* 4.2 6.7 - - + -
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Residues in contact with ASP 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A TYR* 6.0 2.3 - - - -
519A ASP* 2.8 20.3 + - - +
520A ALA 3.8 0.2 - - - +
522A ILE* 1.4 77.0 - - - +
524A GLN* 1.4 53.2 + - - +
526A ALA* 3.1 3.0 + - - +
527A GLU* 2.8 31.4 + - - +
586A TYR* 3.4 24.2 + - - +
588A GLN* 3.3 37.2 + - - +
589A MET* 4.2 5.7 + - - +
590A PHE* 5.2 3.3 + - - -
591A GLY 5.3 0.7 + - - -
722A ARG* 2.4 32.2 + - - +
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Residues in contact with GLN 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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520A ALA 2.9 18.6 + - - +
521A VAL 3.2 4.7 + - - +
523A ASP* 1.4 72.6 + - - +
525A CYS* 1.3 63.2 + - - +
527A GLU* 3.3 17.8 + - - +
528A HIS* 3.0 34.6 + - + -
722A ARG* 3.1 50.0 + - + +
725A VAL* 3.7 17.7 - - + -
726A ASP* 3.1 28.8 + - - +
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Residues in contact with CYS 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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521A VAL* 3.0 22.8 + - - -
522A ILE 3.6 5.8 - - - +
523A ASP 3.3 0.4 - - - -
524A GLN* 1.3 73.7 - - - +
526A ALA* 1.4 62.4 + - - +
528A HIS* 3.2 7.7 + - - -
529A GLY 3.3 0.2 + - - -
530A LEU* 3.1 35.1 + - + +
533A VAL* 3.9 13.0 - - + -
595A ILE* 3.6 21.1 - - + -
638A VAL* 3.8 31.0 - - - -
725A VAL* 3.9 21.8 - - - -
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Residues in contact with ALA 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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522A ILE 3.1 13.0 + - - +
523A ASP* 3.1 10.7 + - - +
525A CYS* 1.4 71.9 - - - +
527A GLU* 1.3 55.5 + - - +
529A GLY* 2.9 11.9 + - - +
530A LEU 4.7 2.5 - - - +
586A TYR* 4.9 1.3 - - + -
588A GLN* 3.7 21.5 - - + -
593A ASN* 2.8 42.0 + - + +
594A ASP 4.7 0.4 - - - -
595A ILE* 3.8 26.4 - - + +
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Residues in contact with GLU 527 (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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523A ASP* 2.8 15.1 + - - +
524A GLN* 3.4 29.2 - - - +
525A CYS 3.3 0.4 - - - -
526A ALA* 1.3 76.8 - - - +
528A HIS* 1.3 58.1 + - + +
529A GLY 3.3 3.1 + - - -
588A GLN* 2.6 33.2 + - - +
591A GLY* 4.2 9.6 - - - -
592A ASP* 5.5 2.5 - - - +
593A ASN* 4.1 8.3 + - - +
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Residues in contact with HIS 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A GLN* 3.0 27.9 + - + +
525A CYS 3.2 9.9 + - - +
527A GLU* 1.3 76.1 - - + +
529A GLY* 1.3 61.3 + - - +
530A LEU* 3.3 17.9 + - + +
634A ARG* 3.3 14.2 + - - -
725A VAL* 4.0 11.7 - - + -
726A ASP* 2.7 33.8 + - - -
729A GLN* 3.5 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
------------------------------------------------------------
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