Contacts of the helix formed by residues 514 - 523 (chain D) in PDB entry 2W93
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 514 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361D ALA 3.3 15.4 + - - +
362D SER* 3.7 22.0 - - - +
363D THR 3.3 8.1 - - - +
364D PRO* 4.8 1.8 - - + -
365D LEU* 3.6 8.5 - - - +
513D ALA* 1.3 88.3 - - + +
515D THR* 1.3 64.7 + - - +
517D GLU* 3.1 34.6 + - - +
518D TRP* 3.0 22.7 + - - +
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Residues in contact with THR 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359D VAL* 3.9 15.4 - - + +
360D PRO 3.1 28.0 - - - +
361D ALA* 3.7 1.6 - - - +
363D THR* 2.8 28.1 + - - +
364D PRO 4.7 2.4 + - - -
365D LEU* 3.9 5.1 - - - +
369D TRP* 3.5 43.8 + - - -
514D THR* 1.3 73.1 - - - +
516D GLY* 1.3 60.7 + - - +
518D TRP* 3.4 1.2 + - - +
519D ASP* 3.0 33.9 + - - +
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Residues in contact with GLY 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D ALA* 2.8 41.8 + - - -
515D THR* 1.3 72.7 - - - +
517D GLU* 1.3 63.2 + - - +
519D ASP* 3.4 4.2 + - - +
520D LYS* 2.9 33.3 + - - +
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Residues in contact with GLU 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511D ARG 3.8 13.5 - - - +
512D VAL* 3.9 15.7 - - + +
513D ALA* 2.9 33.1 + - - +
514D THR* 3.1 26.4 + - - +
516D GLY* 1.3 74.0 - - - +
518D TRP* 1.3 62.8 + - - +
520D LYS* 4.0 3.4 - - - +
521D LEU* 3.1 27.7 + - - +
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Residues in contact with TRP 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D LEU* 3.9 15.5 - - + -
369D TRP* 3.6 23.6 - + + -
370D MET* 3.6 41.1 - - + -
373D GLN* 3.9 17.2 + - + +
374D LEU* 4.0 24.6 - - + +
377D PHE* 5.6 1.2 - - + +
441D PHE* 4.0 12.6 - + - -
467D PHE* 4.0 25.1 - + - -
512D VAL* 3.9 24.3 - - + +
514D THR 3.0 16.4 + - - +
515D THR 3.6 4.3 - - - +
517D GLU* 1.3 77.3 - - - +
519D ASP* 1.3 70.6 + - - +
522D THR* 2.8 53.7 + - + +
536D ILE* 5.8 0.2 - - + -
538D VAL* 4.1 12.8 - - + -
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Residues in contact with ASP 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369D TRP* 3.7 6.3 - - - -
373D GLN* 2.8 39.9 + - - +
376D ASN* 5.2 0.2 + - - -
515D THR* 3.0 20.4 + - - +
516D GLY* 4.0 4.9 - - - +
518D TRP* 1.3 78.2 - - - +
520D LYS* 1.3 63.3 + - + +
522D THR* 3.9 3.8 + - - -
523D GLN* 2.9 59.8 + - - +
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Residues in contact with LYS 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D ALA* 6.4 0.2 - - - +
516D GLY* 2.9 22.5 + - - +
517D GLU* 4.3 2.7 - - - +
519D ASP* 1.3 81.4 - - - +
521D LEU* 1.3 64.3 + - - +
523D GLN* 4.2 14.6 - - + +
524D ASP* 3.4 20.6 + - - +
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Residues in contact with LEU 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510D HIS* 3.5 50.5 - - + +
512D VAL* 3.9 16.8 - - + -
517D GLU 3.1 18.4 + - - +
518D TRP 4.0 1.8 - - - +
520D LYS* 1.3 76.7 - - - +
522D THR* 1.3 64.5 + - + +
524D ASP* 3.1 25.2 + - + +
527D PHE* 3.3 51.1 - - + +
536D ILE* 4.1 10.1 - - + -
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Residues in contact with THR 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376D ASN* 6.1 0.9 - - - +
377D PHE* 3.5 31.9 - - + +
467D PHE* 4.6 11.7 - - + -
518D TRP* 2.8 61.2 + - + +
519D ASP* 3.7 4.2 + - - -
521D LEU* 1.3 82.2 - - + +
523D GLN* 1.3 62.4 + - - +
524D ASP 3.3 0.4 - - - -
527D PHE* 3.9 19.7 - - + -
528D ASN* 2.9 19.8 + - - +
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Residues in contact with GLN 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373D GLN* 5.1 2.8 - - - +
376D ASN* 5.1 13.3 - - + +
519D ASP* 2.9 52.5 + - - +
520D LYS* 4.2 15.6 - - + +
522D THR* 1.3 80.7 - - - +
524D ASP* 1.3 63.7 + - - +
525D LYS* 3.5 3.1 + - - -
528D ASN* 3.9 3.4 + - - +
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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