Contacts of the helix formed by residues 559 - 568 (chain A) in PDB entry 2HWK
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 ASN 559 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A FMT 3.6 10.2 - - - +
531A GLY 3.6 17.3 - - - +
532A LEU 2.9 8.3 + - - +
534A SER* 3.0 21.6 + - - -
535A ALA* 3.9 18.3 - - - +
558A LEU* 1.3 71.1 - - - +
560A LYS* 1.3 58.7 + - - +
561A GLU* 3.1 22.3 + - - +
562A VAL* 3.2 21.8 + - + +
563A VAL* 3.1 28.3 + - - +
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Residues in contact with LYS 560 (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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101A FMT 3.0 24.9 + - - +
558A LEU* 4.8 18.4 - - + +
559A ASN* 1.3 69.2 + - - +
561A GLU* 1.3 65.9 + - - +
563A VAL* 3.3 8.6 + - + +
564A ARG* 3.0 45.1 + - - +
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Residues in contact with GLU 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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101A FMT 3.9 6.0 + - - +
559A ASN* 3.1 9.8 + - - +
560A LYS* 1.3 76.9 - - - +
562A VAL* 1.3 60.3 + - + +
564A ARG* 3.3 31.4 + - + +
565A GLN* 2.9 48.9 + - + +
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Residues in contact with VAL 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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530A SER 3.5 23.3 - - - +
531A GLY* 3.6 13.5 - - - +
532A LEU* 3.9 11.2 - - - +
534A SER* 4.4 1.3 - - - +
559A ASN* 3.2 34.2 + - + +
561A GLU* 1.3 77.6 - - + +
563A VAL* 1.3 60.7 + - - +
565A GLN* 3.3 8.7 + - + +
566A LEU* 2.9 47.4 + - + +
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Residues in contact with VAL 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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532A LEU* 3.5 25.1 - - + -
558A LEU* 3.7 17.7 - - + -
559A ASN 3.1 19.0 + - - +
560A LYS* 3.6 10.3 - - + +
561A GLU 3.3 0.4 - - - -
562A VAL* 1.3 77.0 - - - +
564A ARG* 1.3 57.3 + - + +
566A LEU* 3.1 6.6 + - - +
567A SER* 2.8 31.1 + - - -
573A LEU* 4.5 6.6 - - + +
574A PRO* 3.9 25.1 - - + -
577A VAL* 3.8 22.4 - - + -
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Residues in contact with ARG 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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101A FMT 5.2 1.6 + - - -
560A LYS* 3.0 40.0 + - - +
561A GLU* 3.5 37.0 + - + +
563A VAL* 1.3 76.9 - - + +
565A GLN* 1.3 67.0 + - - +
567A SER* 2.5 26.1 + - - -
568A ARG* 3.8 3.3 + - - +
574A PRO* 5.7 0.9 - - - -
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Residues in contact with GLN 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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561A GLU* 2.9 43.5 + - + +
562A VAL* 3.3 10.1 + - + +
564A ARG* 1.3 78.3 - - - +
566A LEU* 1.3 63.2 + - + +
567A SER 3.5 0.2 + - - -
568A ARG* 3.5 12.9 - - - +
569A ARG* 3.5 18.7 + - - +
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Residues in contact with LEU 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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526A LEU* 3.7 29.8 - - + -
530A SER* 4.8 9.6 - - - +
532A LEU* 4.1 11.7 - - + -
562A VAL* 2.9 43.1 + - + +
563A VAL 3.8 3.1 - - - +
565A GLN* 1.3 74.6 - - + +
567A SER* 1.3 60.1 + - - +
568A ARG 3.0 2.7 - - - -
569A ARG* 3.0 14.1 + - - +
570A TYR* 2.8 49.5 + - + -
573A LEU* 3.8 19.1 - - + -
603A ASN* 6.4 0.7 - - + -
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Residues in contact with SER 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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563A VAL 2.8 13.5 + - - -
564A ARG* 2.5 25.5 + - - +
566A LEU* 1.3 73.4 - - - +
568A ARG* 1.3 64.6 + - - +
569A ARG 3.3 0.2 - - - -
570A TYR 3.4 11.7 - - - -
571A PRO* 3.0 26.8 - - - +
573A LEU* 5.2 0.2 - - - -
574A PRO* 3.5 30.0 - - - +
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Residues in contact with ARG 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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564A ARG 3.8 2.2 + - - +
565A GLN* 3.5 14.7 + - - +
566A LEU 3.0 0.2 - - - -
567A SER* 1.3 83.9 + - - +
569A ARG* 1.3 96.2 + - - +
571A PRO* 4.4 4.7 - - - +
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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