Contacts of the helix formed by residues 560 - 572 (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 MET 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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552A ASN* 4.0 6.1 - - - +
554A ASN* 3.4 37.0 - - - +
556A LEU 3.3 15.9 - - - +
557A GLU* 3.9 20.6 + - - +
558A SER 4.0 0.4 - - - -
559A TYR* 1.3 75.7 - - - +
561A LYS* 1.3 66.5 + - - +
562A GLU* 3.4 8.3 - - + +
563A LYS* 3.4 13.5 + - + +
564A LEU* 3.0 22.9 + - - +
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Residues in contact with LYS 561 (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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549A ILE* 3.3 29.3 + - + +
550A TYR* 3.2 24.2 + - - +
552A ASN* 3.2 35.6 + - + +
554A ASN* 3.0 28.8 + - - +
560A MET* 1.3 70.7 - - - +
562A GLU* 1.3 61.7 + - + +
564A LEU* 3.3 6.9 + - - +
565A LYS* 3.2 37.4 + - - +
627A ALA* 6.3 2.5 - - - -
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Residues in contact with GLU 562 (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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560A MET* 3.4 7.8 - - + +
561A LYS* 1.3 75.8 - - - +
563A LYS* 1.3 64.7 + - - +
565A LYS* 2.7 37.7 + - - +
566A GLN* 3.1 55.5 + - - +
574A LYS* 5.5 3.1 + - - -
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Residues in contact with LYS 563 (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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557A GLU 5.0 4.0 - - - +
558A SER 3.4 25.8 + - - +
559A TYR* 3.8 25.9 - - + -
560A MET* 3.4 17.9 + - + +
561A LYS 3.3 0.2 - - - -
562A GLU* 1.3 79.4 - - - +
564A LEU* 1.3 57.1 + - - +
566A GLN* 3.5 13.3 + - - +
567A LEU* 2.9 45.3 + - + +
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Residues in contact with LEU 564 (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 LEU* 4.2 11.2 - - + -
519A VAL* 4.1 21.5 - - + -
545A LEU* 4.6 10.5 - - + +
548A SER* 4.1 12.1 - - - +
549A ILE* 3.6 21.8 - - + -
552A ASN* 3.5 28.5 - - - +
559A TYR* 3.6 37.9 - - + +
560A MET 3.0 15.9 + - - +
561A LYS 3.5 6.1 - - - +
562A GLU 3.3 0.2 - - - -
563A LYS* 1.3 74.1 - - - +
565A LYS* 1.3 62.1 + - - +
567A LEU* 3.4 8.6 - - + +
568A ILE* 3.2 25.6 + - - +
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Residues in contact with LYS 565 (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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549A ILE* 4.2 22.9 - - + -
561A LYS* 3.2 22.4 + - - +
562A GLU* 2.7 45.4 + - - +
563A LYS 3.3 0.2 - - - -
564A LEU* 1.3 72.0 - - - +
566A GLN* 1.3 61.3 + - - +
568A ILE* 3.1 8.8 + - - +
569A GLU* 2.9 27.0 + - - +
574A LYS* 3.9 19.5 - - - +
627A ALA* 3.1 28.5 - - - +
628A ILE* 3.8 21.3 - - + +
629A TYR 4.8 9.7 + - - +
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Residues in contact with GLN 566 (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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562A GLU* 3.1 41.6 + - - +
563A LYS* 3.7 12.9 - - + +
565A LYS* 1.3 73.4 - - + +
567A LEU* 1.3 58.5 + - + +
569A GLU* 3.7 8.3 - - + +
570A LYS* 2.9 31.7 + - - +
574A LYS* 6.3 0.4 - - - +
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Residues in contact with LEU 567 (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* 4.2 20.2 - - + -
520A PRO* 5.9 2.2 - - + -
523A THR* 4.1 21.1 - - + +
545A LEU* 6.5 0.4 - - + -
559A TYR* 4.7 9.4 - - + +
563A LYS* 2.9 41.5 + - + +
564A LEU* 3.4 15.3 - - + +
565A LYS 3.3 0.2 - - - -
566A GLN* 1.3 73.6 - - + +
568A ILE* 1.3 60.3 + - + +
570A LYS* 4.9 5.4 - - + -
571A ARG* 2.8 56.1 + - + +
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Residues in contact with ILE 568 (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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523A THR* 5.7 0.9 - - - +
545A LEU* 3.9 23.1 - - + -
549A ILE* 3.4 33.4 - - + -
564A LEU 3.2 6.7 + - - +
565A LYS* 3.1 9.6 + - - +
567A LEU* 1.3 73.4 - - + +
569A GLU* 1.3 59.9 + - - +
572A ILE* 2.8 20.0 + - + -
573A GLY 2.7 28.7 + - - +
574A LYS* 4.0 17.5 - - + -
577A PHE* 3.5 53.2 - - + -
628A ILE* 4.2 10.1 - - + -
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Residues in contact with GLU 569 (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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565A LYS 2.9 15.4 + - - +
566A GLN* 3.7 9.4 - - - +
568A ILE* 1.3 80.6 - - - +
570A LYS* 1.3 61.1 + - - +
573A GLY* 3.2 18.6 + - - +
574A LYS* 3.4 46.8 + - + +
575A GLU* 4.2 9.7 - - - +
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Residues in contact with LYS 570 (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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566A GLN 2.9 18.9 + - - +
567A LEU* 4.2 6.3 - - + +
569A GLU* 1.3 78.8 - - - +
571A ARG* 1.3 98.8 + - + +
572A ILE 3.8 0.2 + - - -
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Residues in contact with ARG 571 (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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523A THR* 3.5 34.1 - - + -
527A ALA* 3.6 15.1 - - - +
567A LEU* 2.8 38.9 + - + +
570A LYS* 1.3 107.3 - - + +
572A ILE* 1.3 61.4 + - + +
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Residues in contact with ILE 572 (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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523A THR* 4.0 21.5 - - - +
526A ILE* 3.8 42.4 - - + +
527A ALA* 3.9 19.1 - - + -
545A LEU* 4.5 1.1 - - + -
568A ILE* 2.8 23.3 + - + +
569A GLU 4.2 0.2 - - - -
570A LYS 3.5 0.6 - - - -
571A ARG* 1.3 90.9 - - + +
573A GLY* 1.3 66.9 + - - +
576A ASN* 3.5 24.5 - - - +
577A PHE* 4.2 23.6 - - + +
580A LYS* 5.2 0.4 - - + -
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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