Contacts of the helix formed by residues 515 - 526 (chain A) in PDB entry 4WTM
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 GLY 515 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511A LEU 3.8 1.4 + - - -
512A ILE 3.0 11.2 + - - -
513A SER 3.4 1.2 - - - -
514A ARG* 1.3 82.9 - - - +
516A GLY* 1.3 69.4 + - - +
518A ALA* 3.4 7.8 + - - +
519A ALA* 3.2 23.3 + - - -
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Residues in contact with GLY 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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515A GLY* 1.3 74.8 - - - +
517A LYS* 1.3 62.8 + - - -
519A ALA* 3.2 7.9 + - - +
520A VAL* 3.4 15.4 + - - +
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Residues in contact with LYS 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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455A ASN* 5.5 2.6 + - - -
457A LEU* 3.8 40.9 - - + +
458A ASP* 2.9 29.0 + - - -
516A GLY* 1.3 71.4 - - - -
518A ALA* 1.3 64.1 + - - +
520A VAL* 3.0 12.6 + - + +
521A CYS* 3.0 23.4 + - - -
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Residues in contact with ALA 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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439A LEU* 4.3 3.6 - - + -
457A LEU* 3.6 24.3 - - + +
511A LEU* 3.5 30.8 - - + +
514A ARG* 4.0 16.4 - - + -
515A GLY 3.4 9.4 + - - +
516A GLY 3.2 0.6 - - - -
517A LYS* 1.3 77.0 - - - +
519A ALA* 1.3 58.5 + - - +
521A CYS* 3.1 7.2 + - - +
522A GLY 3.0 23.4 + - - -
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Residues in contact with ALA 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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511A LEU 3.4 7.8 + - - -
512A ILE* 3.6 19.8 - - - +
515A GLY* 3.2 31.7 + - - -
516A GLY 3.7 2.9 - - - +
517A LYS 3.2 0.2 - - - -
518A ALA* 1.3 81.5 - - - +
520A VAL* 1.3 55.9 + - + +
522A GLY* 3.3 1.6 + - - -
523A ARG* 3.0 52.1 + - - +
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Residues in contact with VAL 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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460A PRO* 4.3 14.8 - - + -
516A GLY 3.4 13.7 + - - +
517A LYS* 3.0 14.0 + - + +
519A ALA* 1.3 74.9 - - - +
521A CYS* 1.3 58.7 + - - +
523A ARG* 3.1 9.3 + - - +
524A TYR* 2.8 54.7 + - + +
539A LEU* 4.2 15.5 - - + -
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Residues in contact with CYS 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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430A PHE* 4.0 33.0 - - + -
457A LEU* 3.8 22.2 - - - -
460A PRO* 3.7 32.5 - - - -
511A LEU* 4.3 5.8 - - + -
517A LYS 3.0 16.7 + - - -
518A ALA* 3.2 9.4 - - - +
520A VAL* 1.3 73.2 - - - +
522A GLY* 1.3 58.4 + - - +
525A LEU* 2.8 41.3 + - + +
526A PHE* 4.0 0.5 + - - -
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Residues in contact with GLY 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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508A ARG* 3.5 16.6 + - - +
511A LEU* 3.7 26.9 - - - +
512A ILE* 4.4 6.3 - - - -
518A ALA 3.0 11.1 + - - -
519A ALA 3.3 4.5 + - - -
520A VAL 3.2 0.2 - - - -
521A CYS* 1.3 77.5 - - - +
523A ARG* 1.3 60.8 + - - +
526A PHE* 3.4 24.7 + - - +
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Residues in contact with ARG 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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508A ARG* 4.6 5.7 + - - +
512A ILE* 4.0 34.5 + - + +
519A ALA* 3.0 43.8 + - - +
520A VAL* 3.1 10.0 + - - +
522A GLY* 1.3 75.9 - - - +
524A TYR* 1.3 74.6 + - + +
527A ASN* 3.3 27.5 + - - +
534A LEU* 3.8 29.6 - - + +
536A LEU* 3.8 7.3 - - + +
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Residues in contact with TYR 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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422A ARG* 5.7 0.3 + - - -
460A PRO* 4.2 15.5 - - + -
469A LEU* 4.1 5.4 - - + -
472A PHE* 3.4 54.2 - + + +
520A VAL* 2.8 37.2 + - + +
521A CYS 4.4 0.2 - - - +
523A ARG* 1.3 85.2 - - + +
525A LEU* 1.3 61.5 + - - +
526A PHE 3.3 0.9 + - - -
527A ASN* 3.9 4.3 + - - +
528A TRP* 5.8 0.2 - - - -
536A LEU* 3.9 30.7 - - + +
537A THR* 2.6 45.4 + - - -
539A LEU* 3.4 31.2 - - + +
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Residues in contact with LEU 525 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422A ARG* 5.2 2.0 + - - -
426A MET* 4.1 26.2 - - + +
430A PHE* 3.4 39.0 - - + -
459A LEU* 4.3 13.5 - - + -
460A PRO* 4.3 10.3 - - + -
463A ILE* 4.0 16.2 - - + -
472A PHE* 3.5 29.6 - - + -
521A CYS* 2.8 31.5 + - + +
524A TYR* 1.3 73.0 - - - +
526A PHE* 1.3 71.7 + - + +
527A ASN 3.7 0.2 - - - -
528A TRP* 3.1 20.9 + - - -
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Residues in contact with PHE 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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422A ARG 4.3 2.5 - - - -
426A MET* 3.7 34.1 - - + -
427A THR* 3.5 28.5 - - - -
430A PHE* 4.2 8.3 - + - -
504A ALA* 4.0 11.4 - - + -
507A VAL* 4.0 11.4 - - + -
508A ARG* 3.2 36.4 - - + -
511A LEU* 3.8 25.8 - - + -
521A CYS 4.0 7.2 - - - -
522A GLY* 3.4 14.7 + - - +
524A TYR 3.3 0.2 - - - -
525A LEU* 1.3 97.5 - - + +
527A ASN* 1.3 58.9 + - - +
528A TRP* 3.1 22.7 - + - +
529A ALA* 2.9 20.3 + - + +
530A VAL 4.1 0.2 + - - -
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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
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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