Contacts of the helix formed by residues 562 - 573 (chain A) in PDB entry 2KHH
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 562 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556A HIS* 3.6 12.2 + - - -
560A LYS 2.9 9.7 + - - -
561A LEU* 1.3 83.2 - - - +
563A ALA* 1.3 64.7 + - - +
564A GLU* 4.2 10.1 + - - +
565A TYR* 3.0 34.8 + - + -
566A THR* 2.4 35.5 + - - -
594A GLU* 3.2 17.4 + - - +
595A ALA 2.8 9.3 + - - +
597A VAL* 3.5 10.5 - - + +
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Residues in contact with ALA 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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552A LEU* 6.2 2.2 - - + -
556A HIS* 3.1 21.4 + - + +
562A ASN* 1.3 74.7 + - - +
564A GLU* 1.3 61.1 + - + +
566A THR* 2.4 42.2 + - + -
567A PHE* 2.6 13.1 + - - -
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Residues in contact with GLU 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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562A ASN* 3.6 6.4 + - - +
563A ALA* 1.3 83.8 - - + +
565A TYR* 1.3 75.9 + - + +
567A PHE* 3.2 19.3 + - - +
568A MET* 3.0 17.7 + - - +
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Residues in contact with TYR 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 LEU* 3.1 26.0 - - + +
562A ASN* 3.0 34.3 - - + -
563A ALA 2.7 3.4 + - - -
564A GLU* 1.3 78.0 - - + +
566A THR* 1.3 58.3 + - - +
567A PHE 3.0 1.6 - - - -
568A MET* 2.5 63.2 + - + +
569A LEU* 2.9 4.3 + - - +
591A ILE* 5.6 1.3 - - + -
592A PRO* 4.3 9.4 - - + -
594A GLU* 3.3 17.8 + - + +
595A ALA* 3.1 29.4 - - + -
1B ASP* 3.3 37.7 + - - -
4B PHE* 5.9 2.0 - + + -
6B PHE* 4.1 2.4 - + + -
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Residues in contact with THR 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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552A LEU* 3.7 31.9 - - + +
555A LEU* 3.1 40.9 + - + +
556A HIS* 3.5 5.0 + - + +
559A THR* 3.9 5.4 - - - +
561A LEU* 3.1 15.3 + - - +
562A ASN 2.4 20.3 + - - -
563A ALA* 2.4 31.6 + - + +
565A TYR 1.3 64.0 - - - -
567A PHE* 1.3 63.4 + - + +
569A LEU* 2.8 21.7 + - - +
570A ALA 2.8 10.9 + - - -
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Residues in contact with PHE 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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544A LEU* 5.7 2.5 - - + -
552A LEU* 4.0 18.8 - - + -
563A ALA 2.6 13.6 + - - +
564A GLU* 3.2 19.7 - - - +
566A THR* 1.3 72.3 - - - +
568A MET* 1.3 69.0 + - + +
569A LEU 2.8 4.5 - - - -
570A ALA* 2.5 30.0 + - - +
571A GLU* 2.6 39.7 + - + +
575A TRP* 3.8 33.7 - + - -
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Residues in contact with MET 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 GLU 3.0 8.8 + - - +
565A TYR* 2.5 63.7 + - + +
567A PHE* 1.3 74.9 - - + +
569A LEU* 1.3 53.9 + - - -
571A GLU* 2.8 34.9 - - - +
572A GLN* 2.8 47.8 + - - +
1B ASP* 4.7 10.3 - - - +
2B SER* 4.0 18.4 - - - +
4B PHE* 3.7 34.5 - - + +
6B PHE* 4.6 1.8 - - + -
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Residues in contact with LEU 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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555A LEU* 3.7 8.1 - - + -
559A THR* 5.0 0.7 - - + -
561A LEU* 3.5 8.3 - - + -
565A TYR 2.9 2.6 + - - -
566A THR* 2.8 16.5 + - - +
567A PHE 2.7 0.6 + - - -
568A MET* 1.3 75.3 - - - +
570A ALA* 1.3 47.8 + - - -
571A GLU 2.9 5.4 - - - -
572A GLN* 4.1 1.1 - - - +
573A SER* 2.3 46.4 + - - -
580A ALA* 3.0 42.4 - - + +
583A GLY* 4.2 1.3 - - - -
584A PHE* 3.1 19.3 - - + +
6B PHE* 2.9 59.6 - - + -
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Residues in contact with ALA 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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551A LEU* 4.5 5.2 - - + -
552A LEU* 3.1 36.8 - - + -
555A LEU* 4.1 8.1 - - + -
566A THR 2.8 6.3 + - - +
567A PHE* 2.5 15.9 + - - +
569A LEU* 1.3 72.7 - - - +
571A GLU* 1.3 49.4 + - - -
573A SER* 3.5 5.4 - - - -
575A TRP* 2.7 60.0 + - + +
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Residues in contact with GLU 571 (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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567A PHE* 2.6 49.1 + - + +
568A MET* 2.8 36.9 - - - +
570A ALA* 1.3 77.9 - - - +
572A GLN* 1.3 64.6 + - + +
573A SER 3.0 6.3 + - - -
574A ASN* 3.2 13.0 + - - +
575A TRP* 3.2 24.2 + - + +
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Residues in contact with GLN 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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568A MET* 2.8 42.8 + - - +
569A LEU* 3.3 2.7 + - - -
571A GLU* 1.3 84.3 - - + +
573A SER* 1.3 58.4 + - - +
574A ASN* 3.4 7.8 + - - +
2B SER* 5.2 1.0 + - - -
3B GLY* 5.0 0.5 - - - -
4B PHE* 2.4 32.9 + - - +
5B SER* 3.3 12.2 - - - +
6B PHE* 3.2 36.3 - - + +
7B GLY* 4.4 16.3 + - - +
9B LYS* 5.2 20.7 - - + +
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Residues in contact with SER 573 (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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569A LEU* 2.3 31.4 + - - -
570A ALA* 3.5 9.4 - - - -
572A GLN* 1.3 78.1 - - - +
574A ASN* 1.3 78.5 + - - +
575A TRP* 3.0 6.8 + - - -
576A ASN* 3.3 4.7 + - - +
579A VAL* 3.0 20.3 - - - +
580A ALA* 3.4 35.9 - - - +
583A GLY* 5.4 1.6 - - - -
7B GLY* 5.6 2.7 - - - +
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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