Contacts of the helix formed by residues 512 - 525 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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508B PHE 3.0 13.5 + - - +
509B PRO 3.5 3.6 - - - -
511B GLU* 1.3 82.0 - - - +
513B PRO* 1.4 65.8 - - - +
515B THR* 4.2 9.6 - - - -
516B VAL* 3.1 25.9 + - + +
565B GLU* 3.3 38.8 - - + +
567B HIS* 5.3 0.2 - - - -
570B LEU* 3.6 15.9 - - - -
607B THR* 4.0 2.9 - - - -
608B VAL 3.3 26.7 - - - -
609B PHE* 4.4 3.1 - - + -
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Residues in contact with PRO 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490B VAL* 3.7 10.4 - - + +
509B PRO* 3.2 15.7 - - + +
510B VAL 3.5 12.6 - - - +
511B GLU 3.6 4.9 - - - +
512B CYS* 1.4 88.2 - - - +
514B LYS* 1.3 73.3 + - + +
517B GLU* 3.1 29.3 + - - +
565B GLU* 3.3 12.6 - - + +
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Residues in contact with LYS 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A PRO 5.4 7.4 - - - -
630A LYS* 5.3 11.0 + - - +
513B PRO* 1.3 84.8 - - + +
515B THR* 1.3 60.9 + - - +
517B GLU* 3.4 14.7 + - - +
518B ASN* 3.0 26.0 + - - +
558B TRP* 3.5 24.2 - - + -
562B PHE* 4.3 12.3 - - + -
565B GLU* 2.8 25.1 + - + +
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Residues in contact with THR 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512B CYS* 4.0 3.1 - - - -
514B LYS* 1.3 74.3 - - - +
516B VAL* 1.3 62.8 + - - +
518B ASN* 3.5 3.1 + - - +
519B PHE* 3.1 22.5 + - - +
562B PHE* 3.8 18.5 - - + -
563B GLU 4.7 1.4 + - - -
565B GLU* 2.6 32.6 + - - +
580B MET* 3.3 36.9 - - + +
588B ASN* 5.7 0.5 + - - -
607B THR* 3.7 16.1 + - + +
609B PHE* 3.6 28.3 - - + -
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Residues in contact with VAL 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B VAL* 4.1 5.4 - - + -
491B SER 3.4 25.6 - - - +
507B LEU* 3.9 9.0 - - + -
508B PHE 3.7 17.3 - - - +
509B PRO* 3.6 28.0 - - + -
512B CYS 3.1 18.0 + - - +
513B PRO 4.2 1.3 - - - +
515B THR* 1.3 78.3 - - - +
517B GLU* 1.3 62.8 + - - +
519B PHE* 3.3 4.8 + - - +
520B CYS* 2.9 34.5 + - - -
609B PHE* 4.1 19.7 - - + +
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Residues in contact with GLU 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A ILE* 5.1 7.3 - - - +
489B ARG* 3.2 43.4 + - + +
490B VAL* 3.8 16.3 - - + +
513B PRO 3.1 20.2 + - - +
514B LYS* 3.7 14.1 - - - +
516B VAL* 1.3 76.5 - - - +
518B ASN* 1.3 63.7 + - - +
520B CYS* 3.9 0.2 - - - -
521B VAL* 3.0 35.6 + - + +
557B ILE* 4.0 9.9 - - + -
558B TRP* 4.0 17.5 + - + -
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Residues in contact with ASN 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B LYS 3.0 17.3 + - - +
515B THR 3.7 5.0 - - - +
517B GLU* 1.3 76.5 - - - +
519B PHE* 1.3 62.9 + - - +
522B HIS* 3.2 41.4 + - - +
528B TYR* 4.4 5.0 + - - -
556B SER* 3.2 7.7 - - - +
557B ILE* 2.8 43.8 - - - +
558B TRP* 3.7 11.1 - - + -
562B PHE* 3.6 15.6 - - + -
580B MET* 4.5 5.5 - - - +
589B GLY 2.9 21.1 - - - +
590B SER* 4.5 0.3 - - - -
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Residues in contact with PHE 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B ALA* 4.0 22.9 - - + -
496B ILE* 4.4 13.7 - - + -
505B THR* 4.9 0.7 - - - -
507B LEU* 4.1 23.6 - - + -
515B THR 3.1 14.2 + - - +
516B VAL* 3.7 3.6 - - - +
518B ASN* 1.3 83.0 - - - +
520B CYS* 1.3 58.6 + - - +
522B HIS* 3.7 2.1 + - - +
523B SER* 2.6 53.6 + - - -
528B TYR* 4.0 19.5 - + - -
578B LEU* 4.8 4.9 - - + -
580B MET* 6.0 1.8 - - - -
592B PHE* 3.7 30.5 - + - -
609B PHE* 3.7 29.6 - + + -
643B ILE* 4.1 15.0 - - + -
645B VAL* 5.7 0.2 - - + -
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Residues in contact with CYS 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B ARG 3.6 19.1 - - - +
490B VAL 4.2 0.2 - - - -
491B SER 3.7 20.0 - - - -
507B LEU* 3.5 30.5 - - - -
516B VAL* 2.9 21.1 + - - +
517B GLU 4.0 0.7 - - - +
519B PHE* 1.3 78.5 - - - +
521B VAL* 1.3 59.3 + - - +
523B SER* 3.5 5.0 + - - -
524B ARG* 3.0 40.1 + - - +
645B VAL* 3.8 18.3 - - + +
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Residues in contact with VAL 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B ARG* 3.8 50.0 - - + +
517B GLU* 3.0 20.6 + - + +
520B CYS* 1.3 73.9 - - - +
522B HIS* 1.3 67.6 + - - +
524B ARG* 3.1 8.9 + - - +
525B ASN* 2.9 48.2 + - - +
557B ILE* 3.7 26.2 - - + -
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Residues in contact with HIS 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B ASN* 3.2 38.1 + - - +
519B PHE 3.8 0.2 - - - +
521B VAL* 1.3 77.8 - - - +
523B SER* 1.3 63.8 + - - +
525B ASN* 3.3 9.1 + - - +
527B TYR* 3.0 67.8 + + + +
528B TYR* 3.4 28.7 - - + -
555B GLU* 2.7 29.5 + - + -
556B SER 3.3 17.6 - - - -
557B ILE* 3.6 10.1 - - + +
590B SER* 4.4 2.0 - - - -
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Residues in contact with SER 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519B PHE* 2.6 31.7 + - - -
520B CYS 3.6 4.9 - - - -
522B HIS* 1.3 75.6 - - - +
524B ARG* 1.3 55.2 + - - +
526B GLY* 2.8 27.4 + - - -
527B TYR 5.0 0.4 - - - +
528B TYR* 3.7 10.1 - - - +
529B ASN* 4.7 2.5 - - - +
643B ILE* 3.6 46.2 - - - +
645B VAL* 3.7 17.9 - - - -
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Residues in contact with ARG 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A TRP* 3.6 61.7 - - + +
489B ARG* 2.9 34.6 + - - +
490B VAL 3.4 15.6 + - - -
491B SER* 4.0 2.4 - - - -
520B CYS* 3.0 30.0 + - - +
521B VAL* 3.7 8.6 - - - +
523B SER* 1.3 76.2 - - - +
525B ASN* 1.3 62.5 + - - +
526B GLY 3.3 3.5 + - - -
643B ILE 5.1 2.0 - - - -
645B VAL* 3.8 40.3 + - + +
646B LYS 4.9 1.8 + - - -
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Residues in contact with ASN 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521B VAL* 2.9 38.5 + - - +
522B HIS* 3.7 10.0 + - - +
523B SER 3.1 0.4 - - - -
524B ARG* 1.3 81.0 - - - +
526B GLY* 1.3 60.3 + - - +
527B TYR* 3.1 8.2 + - + +
557B ILE* 5.3 2.4 - - - +
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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