Contacts of the helix formed by residues 517 - 528 (chain A) in PDB entry 2W3C
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 ALA 517 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476A GLN* 5.2 2.7 - - - +
480A ASN* 6.1 0.2 - - - +
515A ASN* 3.0 17.9 + - - +
516A SER* 1.3 79.4 + - - +
518A ASN* 1.3 64.0 + - - +
520A PRO* 4.0 4.8 - - - +
521A PHE* 3.3 22.5 + - - +
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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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476A GLN* 3.2 37.5 + - - -
479A THR* 3.4 18.1 - - - +
512A PHE* 2.6 55.5 + - + +
515A ASN* 3.2 15.0 + - - +
516A SER 3.2 0.2 - - - -
517A ALA* 1.3 79.2 - - - +
519A VAL* 1.3 68.3 + - + +
521A PHE* 3.1 8.2 + - - +
522A LEU* 3.0 27.4 + - - +
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Residues in contact with VAL 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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512A PHE* 5.5 1.8 - - + -
513A LEU* 3.5 32.5 - - + -
515A ASN 4.7 1.0 + - - -
516A SER 4.6 0.4 + - - -
518A ASN* 1.3 76.2 - - + +
520A PRO* 1.4 72.2 - - + +
522A LEU* 3.2 8.1 + - + +
523A THR* 3.0 26.9 + - - +
545A LEU* 4.5 13.0 - - + +
559A TYR* 3.7 40.8 - - + +
564A LEU* 4.1 15.9 - - + -
567A LEU* 4.2 17.5 - - + -
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Residues in contact with PRO 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A SER 3.1 26.5 - - - +
517A ALA* 4.0 4.5 - - - +
518A ASN 3.7 1.3 - - - -
519A VAL* 1.4 93.5 - - + +
521A PHE* 1.3 58.0 + - - +
523A THR* 3.9 8.7 - - + +
524A GLY* 3.2 18.5 + - - -
559A TYR* 3.6 13.0 - - - +
567A LEU* 6.1 1.6 - - + -
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Residues in contact with PHE 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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479A THR* 4.9 12.6 - - + -
482A LEU* 3.6 46.7 - - + -
483A SER* 3.7 28.9 - - - -
517A ALA 3.3 15.4 + - - +
518A ASN* 3.1 11.0 + - - +
520A PRO* 1.3 77.1 - - - +
522A LEU* 1.3 84.6 + - + +
524A GLY* 3.1 2.5 + - - -
525A GLN* 3.0 56.1 + - + +
537A VAL* 6.4 0.9 - - + -
541A CYS* 4.6 4.0 - - - -
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Residues in contact with LEU 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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479A THR* 6.1 0.2 - - + -
482A LEU* 5.2 1.3 - - + -
495A LEU* 5.0 1.8 - - + -
512A PHE* 3.8 30.1 - - + -
518A ASN 3.0 18.1 + - - +
519A VAL* 3.2 5.1 + - + +
521A PHE* 1.3 89.9 - - + +
523A THR* 1.3 63.5 + - - +
524A GLY 3.2 0.2 + - - -
525A GLN* 3.3 3.5 + - - +
526A ILE* 2.9 39.8 + - + +
541A CYS* 3.9 31.0 - - + -
544A LEU* 4.2 15.3 - - + -
545A LEU* 3.9 39.5 - - + +
548A SER* 4.9 0.4 - - - +
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Residues in contact with THR 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 VAL* 3.0 20.9 + - - +
520A PRO* 3.9 8.7 - - + +
522A LEU* 1.3 74.9 - - - +
524A GLY* 1.3 57.8 - - - +
526A ILE* 4.2 1.0 - - - +
527A ALA* 3.0 35.7 + - + +
545A LEU* 4.3 12.3 - - - +
567A LEU* 4.1 19.4 + - + +
571A ARG* 3.5 42.2 - - + +
572A ILE* 4.0 14.9 - - + +
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Residues in contact with GLY 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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520A PRO 3.2 12.6 + - - -
521A PHE* 3.1 8.3 + - - -
523A THR* 1.3 76.3 - - - +
525A GLN* 1.3 64.1 - - - +
527A ALA* 3.5 3.5 + - - +
528A GLU* 3.2 34.2 + - - +
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Residues in contact with GLN 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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482A LEU 4.6 2.0 + - - -
483A SER* 5.7 0.6 - - - +
491A ARG* 3.7 24.9 + - - +
521A PHE* 3.0 51.3 + - + +
522A LEU 3.7 2.9 - - - +
524A GLY* 1.3 75.9 - - - +
526A ILE* 1.3 52.0 + - - +
527A ALA 3.6 0.2 + - - -
528A GLU* 3.9 14.4 + - - +
534A GLU* 4.6 10.5 - - - +
537A VAL* 4.3 12.2 - - - +
538A GLN* 2.7 41.9 + - + +
541A CYS* 4.2 14.4 - - - -
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Residues in contact with ILE 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 LEU 2.9 28.9 + - - +
523A THR 4.2 0.2 - - - +
525A GLN* 1.3 76.5 - - - +
527A ALA* 1.3 60.7 + - - +
538A GLN* 3.4 19.8 + - - +
541A CYS* 3.6 16.6 - - + +
542A ALA* 3.5 35.9 - - + +
545A LEU* 3.8 20.0 - - + -
572A ILE* 3.8 26.8 - - + +
577A PHE* 4.2 12.3 - - + -
580A LYS* 3.4 35.1 - - + +
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Residues in contact with ALA 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A THR* 3.0 21.5 + - + +
524A GLY* 3.5 3.8 + - - +
525A GLN 3.3 0.6 - - - -
526A ILE* 1.3 77.3 - - - +
528A GLU* 1.3 59.8 + - - +
529A ASN 3.7 2.8 + - - -
571A ARG 3.6 24.0 - - - +
572A ILE* 3.9 16.4 - - + -
576A ASN* 5.1 6.0 - - - +
580A LYS* 5.6 1.6 + - - -
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Residues in contact with GLU 528 (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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524A GLY 3.2 23.1 + - - +
525A GLN* 4.0 14.6 + - - +
526A ILE 3.5 0.4 - - - -
527A ALA* 1.3 78.6 - - - +
529A ASN* 1.3 63.6 + - - +
530A LEU* 3.1 8.7 + - + +
538A GLN* 2.6 26.8 + - - -
580A LYS* 5.2 0.7 - - - -
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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