Contacts of the helix formed by residues 513 - 526 (chain A) in PDB entry 2WMH
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 LYS 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A TRP* 3.5 10.1 - - - -
509A SER 3.9 12.1 + - - +
510A LYS* 3.0 35.8 + - + +
511A SER 3.7 13.1 + - - +
512A TRP* 1.3 84.6 - - - +
514A LYS* 1.3 67.6 + - - +
515A GLU* 3.2 9.6 - - - +
516A GLU* 3.1 12.3 + - - +
517A LEU 3.4 7.4 + - - -
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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 LYS* 1.3 76.6 - - - +
515A GLU* 1.3 80.9 + - - +
517A LEU* 3.1 18.5 + - + +
518A GLU* 2.9 60.3 + - + +
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Residues in contact with GLU 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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272A MET* 4.3 5.4 - - + +
505A ASN* 3.4 30.9 + - + +
506A PHE* 4.4 5.1 - - + -
510A LYS* 3.5 48.4 + - + +
513A LYS* 3.2 3.8 + - - +
514A LYS* 1.3 103.2 + - + +
516A GLU* 1.3 61.5 + - - +
518A GLU* 3.2 19.4 + - - +
519A LEU* 3.1 22.3 + - - +
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Residues in contact with GLU 516 (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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62A TRP* 3.1 13.5 + - + +
63A TRP* 3.5 28.9 - - - +
253A TRP* 4.9 1.9 - - - -
272A MET* 3.7 15.1 - - - +
275A TYR* 2.7 37.9 + - - +
302A CYS* 4.7 0.2 - - - -
510A LYS 3.5 16.9 + - - +
511A SER* 3.5 9.5 + - - -
512A TRP* 2.7 34.0 + - - -
513A LYS 3.1 6.8 + - - +
515A GLU* 1.3 76.4 - - - +
517A LEU* 1.3 65.0 + - - +
519A LEU* 3.2 6.2 + - + +
520A ALA* 3.0 20.7 + - - +
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Residues in contact with LEU 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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55A ASN* 6.0 0.2 - - - +
62A TRP* 3.3 54.3 - - + +
63A TRP* 3.9 22.2 - - + +
64A GLY 4.7 3.8 - - - +
513A LYS 3.4 1.9 + - - +
514A LYS* 3.1 18.0 + - + +
516A GLU* 1.3 76.8 - - - +
518A GLU* 1.3 53.1 + - + +
520A ALA* 3.1 4.9 + - + +
521A ASN* 2.7 50.7 + - - +
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Residues in contact with GLU 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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506A PHE* 5.1 5.8 - - + -
514A LYS* 2.9 46.1 + - + +
515A GLU* 3.5 21.4 - - - +
516A GLU 3.2 0.2 - - - -
517A LEU* 1.3 76.4 - - + +
519A LEU* 1.3 56.8 + - - +
521A ASN* 3.2 13.3 + - - +
522A TRP* 3.0 28.6 + - - +
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Residues in contact with LEU 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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272A MET* 3.9 40.4 - - + +
273A ARG* 4.1 23.1 - - + +
275A TYR* 4.3 16.2 - - + +
276A ALA* 5.4 0.9 - - + -
499A MET* 4.3 19.1 - - + -
502A LEU* 5.1 1.6 - - + -
506A PHE* 4.0 23.4 - - + -
515A GLU 3.1 12.2 + - - +
516A GLU* 3.2 9.2 + - - +
518A GLU* 1.3 75.5 - - - +
520A ALA* 1.3 59.1 + - - +
522A TRP* 3.3 10.3 + - + +
523A ILE* 3.0 42.2 + - + +
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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
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63A TRP* 3.6 35.9 - - + +
304A ALA* 4.8 1.8 - - + -
309A THR* 2.8 42.3 + - + -
310A ASN* 3.9 0.8 + - - +
516A GLU 3.0 10.2 + - - +
517A LEU* 3.5 10.3 - - + +
519A LEU* 1.3 76.6 - - - +
521A ASN* 1.3 64.3 + - - +
523A ILE* 3.4 5.4 + - - +
524A SER* 3.2 8.7 + - - -
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Residues in contact with ASN 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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310A ASN* 3.1 29.2 + - - +
517A LEU* 2.7 34.6 + - - +
518A GLU* 3.6 11.6 - - - +
520A ALA* 1.3 72.3 - - - +
522A TRP* 1.3 64.2 + - - +
524A SER* 3.0 16.8 + - - -
525A LYS* 3.4 13.8 + - + +
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Residues in contact with TRP 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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498A ALA* 4.3 12.1 - - + -
499A MET* 3.7 43.3 - - + -
502A LEU* 3.5 46.6 - - + +
506A PHE* 6.2 0.4 - - + -
518A GLU 3.0 12.7 + - - +
519A LEU* 3.6 12.8 - - + +
521A ASN* 1.3 76.1 - - - +
523A ILE* 1.3 73.8 + - + +
525A LYS* 3.1 2.3 + - - -
526A ASN* 2.9 73.5 + - + +
527A TYR* 4.2 17.9 - - + -
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Residues in contact with ILE 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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275A TYR* 5.4 1.3 - - + -
276A ALA* 4.6 17.7 - - + -
304A ALA* 3.9 31.4 - - + +
305A TYR* 5.1 0.9 - - - -
309A THR* 3.8 10.5 - - - +
314A THR* 4.2 3.4 - - + -
499A MET* 5.1 2.9 - - - -
519A LEU* 3.0 41.1 + - + +
520A ALA* 3.6 8.7 - - - +
521A ASN 3.3 0.2 - - - -
522A TRP* 1.3 92.6 - - + +
524A SER* 1.3 61.7 + - - +
525A LYS 3.2 0.5 + - - -
527A TYR* 3.4 25.4 + - + -
528A SER* 2.9 42.5 + - - +
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Residues in contact with SER 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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309A THR* 3.4 27.6 - - - -
310A ASN* 2.9 29.5 + - - +
312A VAL* 4.1 12.0 - - - +
520A ALA 3.2 5.5 + - - -
521A ASN 3.0 11.3 + - - -
522A TRP 3.3 0.2 - - - -
523A ILE* 1.3 76.2 - - - +
525A LYS* 1.3 68.4 + - - +
526A ASN 3.7 0.2 - - - -
528A SER* 4.2 9.3 - - - -
529A ILE* 2.9 27.2 - - - +
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Residues in contact with LYS 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 ASN* 3.4 15.2 + - + +
522A TRP* 3.1 2.1 + - - -
524A SER* 1.3 87.5 - - - +
526A ASN* 1.3 73.4 + - - +
529A ILE* 4.3 14.8 - - + +
530A ASN* 4.2 11.6 - - - +
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Residues in contact with ASN 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 TRP* 2.9 71.4 + - + +
523A ILE 3.5 0.4 + - - -
525A LYS* 1.3 90.3 + - - +
527A TYR* 1.3 70.3 + - - +
528A SER 3.1 1.0 + - - -
530A ASN* 2.7 36.5 + - - +
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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