Contacts of the helix formed by residues 512 - 525 (chain A) in PDB entry 2A2N
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 CYS 512 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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508A PHE 2.9 12.9 + - - +
509A PRO 3.7 2.7 - - - -
511A GLU* 1.3 81.2 - - - +
513A PRO* 1.3 65.7 - - - +
515A THR* 3.9 10.3 - - - -
516A VAL* 2.9 22.5 + - - +
565A GLU* 3.1 40.8 - - + +
567A HIS* 5.4 0.2 - - - -
570A LEU* 3.7 15.0 - - - -
607A THR* 4.0 2.7 - - - -
608A VAL 3.3 26.7 - - - -
609A PHE* 4.3 6.7 - - + -
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Residues in contact with PRO 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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490A VAL* 3.8 8.9 - - + +
509A PRO* 3.2 17.0 - - + +
510A VAL 3.5 11.4 - - - +
511A GLU 3.3 9.0 - - - +
512A CYS* 1.3 88.3 - - - +
514A LYS* 1.3 71.1 + - + +
517A GLU* 2.9 32.8 + - - +
565A GLU* 3.2 11.2 - - - +
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Residues in contact with LYS 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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513A PRO* 1.3 87.7 - - + +
515A THR* 1.3 59.1 + - - +
517A GLU* 4.5 7.6 - - - +
518A ASN* 2.9 25.6 + - - +
558A TRP* 3.3 33.1 - - + -
562A PHE* 4.1 15.0 - - + -
563A GLU* 5.0 10.5 - - + +
565A GLU* 3.1 19.1 + - + +
629C PRO 4.5 16.8 + - - -
630C LYS* 5.3 6.4 + - - +
632C ASP* 6.0 2.0 - - - -
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Residues in contact with THR 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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512A CYS* 3.9 9.0 - - - -
514A LYS* 1.3 74.7 - - - +
516A VAL* 1.3 64.5 + - - +
518A ASN* 3.4 3.3 + - - +
519A PHE* 3.1 22.3 + - - +
562A PHE* 3.6 18.6 - - + -
563A GLU 4.7 0.5 + - - -
565A GLU* 2.6 27.6 + - - +
580A MET* 3.5 24.4 - - + +
607A THR* 3.5 15.2 + - + +
609A PHE* 3.4 36.8 - - + -
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Residues in contact with VAL 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A VAL* 4.1 1.6 - - + -
491A SER 3.4 27.8 - - - +
507A LEU* 4.0 10.1 - - + -
508A PHE 3.6 32.3 - - - +
509A PRO* 3.7 15.0 - - + -
512A CYS 2.9 20.5 + - - +
513A PRO 4.3 0.9 - - - +
515A THR* 1.3 72.8 - - - +
517A GLU* 1.3 60.4 + - - +
519A PHE* 3.2 4.6 + - - +
520A CYS* 2.7 46.7 + - - +
609A PHE* 4.0 19.1 - - + +
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Residues in contact with GLU 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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489A ARG* 2.9 44.2 + - + +
490A VAL* 3.6 15.6 - - + +
513A PRO 2.9 20.4 + - - +
514A LYS* 3.7 12.1 - - - +
516A VAL* 1.3 76.4 - - - +
518A ASN* 1.3 64.1 + - - +
520A CYS* 4.5 2.9 - - - -
521A VAL* 2.8 42.5 + - + +
557A ILE* 4.1 2.2 - - + -
558A TRP* 3.6 20.0 + - + -
537C ILE* 4.5 10.2 - - - +
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Residues in contact with ASN 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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514A LYS 2.9 18.2 + - - +
515A THR 3.6 5.3 - - - +
517A GLU* 1.3 75.5 - - - +
519A PHE* 1.3 58.6 + - - +
522A HIS* 3.0 42.1 + - - +
528A TYR* 4.4 2.6 + - - -
556A SER* 3.2 11.9 - - - +
557A ILE* 2.7 50.2 - - - +
558A TRP* 4.0 4.0 - - + -
562A PHE* 3.5 18.4 - - + -
580A MET* 4.1 7.1 - - - +
589A GLY 2.8 21.6 - - - +
590A SER* 4.3 1.6 - - - -
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Residues in contact with PHE 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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494A ALA* 4.1 23.6 - - + -
496A ILE* 4.4 13.5 - - + -
505A THR* 4.8 0.9 - - - -
507A LEU* 4.1 24.0 - - + -
515A THR 3.1 14.3 + - - +
516A VAL* 3.7 3.6 - - - +
518A ASN* 1.3 82.0 - - - +
520A CYS* 1.3 61.8 + - - +
522A HIS* 3.7 1.9 - - - +
523A SER* 2.9 50.4 + - - -
528A TYR* 4.0 18.2 - + - -
578A LEU* 4.7 5.8 - - + -
580A MET* 6.0 1.6 - - - -
592A PHE* 3.8 33.2 - + - -
609A PHE* 3.6 31.2 - + + -
643A ILE* 4.0 15.0 - - + -
645A VAL* 5.5 0.2 - - + -
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Residues in contact with CYS 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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489A ARG 3.4 20.9 - - - +
491A SER 3.7 23.6 - - - -
507A LEU* 3.8 22.9 - - - -
516A VAL* 2.7 26.3 + - - +
517A GLU 3.9 0.7 - - - +
519A PHE* 1.3 74.6 - - - +
521A VAL* 1.3 56.7 + - - +
523A SER* 3.2 6.4 + - - -
524A ARG* 2.9 40.2 + - - +
645A VAL* 3.8 21.3 - - + -
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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
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489A ARG* 3.5 52.3 - - + +
517A GLU* 2.8 25.6 + - + +
520A CYS* 1.3 69.7 - - - +
522A HIS* 1.3 65.8 + - - +
524A ARG* 4.0 7.2 - - - +
525A ASN* 3.0 36.5 + - - +
557A ILE* 3.8 20.2 - - + -
401C GOL 3.1 28.0 - - - +
601C TRP* 6.4 0.4 - - + -
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Residues in contact with HIS 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 ASN* 3.0 36.3 + - - +
519A PHE 3.7 0.2 - - - +
521A VAL* 1.3 77.5 - - - +
523A SER* 1.3 61.5 + - - +
525A ASN* 3.3 6.3 + - - +
526A GLY 3.1 4.0 + - - -
527A TYR* 2.9 66.0 + + + +
528A TYR* 3.4 33.4 - - + -
555A GLU* 2.8 28.7 + - + -
556A SER 4.0 2.5 - - - -
557A ILE* 3.6 24.8 + - + +
590A SER* 4.1 5.6 - - - -
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Residues in contact with SER 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 PHE* 2.9 30.3 + - - -
520A CYS* 3.5 5.2 - - - -
522A HIS* 1.3 75.8 - - - +
524A ARG* 1.3 61.6 + - - +
526A GLY* 3.0 15.1 + - - -
527A TYR 5.1 0.4 - - - +
528A TYR* 3.8 8.7 - - - +
529A ASN* 4.7 3.3 - - - +
643A ILE* 3.3 49.4 + - - +
645A VAL* 3.6 19.3 - - - -
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Residues in contact with ARG 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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489A ARG* 2.8 40.2 + - - +
490A VAL 3.7 12.1 + - - -
491A SER* 4.3 1.8 - - - -
520A CYS* 2.9 27.0 + - - +
521A VAL* 4.1 6.9 - - - +
523A SER* 1.3 75.4 - - - +
525A ASN* 1.3 62.9 + - - +
526A GLY 3.1 1.7 + - - -
643A ILE 5.0 1.8 - - - -
645A VAL* 3.6 41.7 + - + +
646A LYS 4.8 3.2 + - - -
601C TRP* 3.6 57.8 - - + +
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Residues in contact with ASN 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 30.7 + - - +
522A HIS* 3.5 10.9 + - - +
524A ARG* 1.3 78.1 - - - +
526A GLY* 1.3 60.0 + - - +
527A TYR* 3.5 5.7 + - + +
557A ILE* 5.3 0.6 - - - +
401C GOL 3.0 29.7 + - - -
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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