Contacts of the helix formed by residues 560 - 571 (chain A) in PDB entry 2H5G
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 SER 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481A GLU* 3.0 18.4 + - - -
559A GLY* 1.3 76.2 - - - +
561A SER* 1.3 53.9 + - - +
562A GLN* 3.4 9.2 + - - +
563A LEU* 2.9 25.1 + - - +
564A VAL* 2.8 33.9 + - - +
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Residues in contact with SER 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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560A SER* 1.3 72.7 - - - +
562A GLN* 1.3 56.5 + - - +
564A VAL* 3.8 6.6 - - - +
565A ARG* 2.8 33.1 + - - +
580A SER* 2.7 33.7 + - - +
581A GLU* 4.9 0.2 - - - -
667A GLU* 5.1 4.5 + - - -
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Residues in contact with GLN 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 SER* 3.1 8.1 + - - +
561A SER* 1.3 75.2 - - - +
563A LEU* 1.3 56.5 + - - +
565A ARG* 3.3 3.5 + - - +
566A ASP* 2.7 37.0 + - - +
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Residues in contact with LEU 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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479A ILE* 4.4 17.0 - - + +
481A GLU* 3.6 37.7 - - + +
542A VAL* 5.4 7.0 - - + -
557A PRO* 5.0 0.7 - - + -
558A ARG 3.9 8.3 - - - +
559A GLY* 3.8 15.3 - - - +
560A SER* 2.9 21.9 + - - +
562A GLN* 1.3 72.2 - - - +
564A VAL* 1.3 58.5 + - - +
566A ASP* 3.1 7.9 + - + +
567A ILE* 2.8 63.2 + - + +
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Residues in contact with VAL 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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557A PRO* 4.0 36.1 - - + +
559A GLY 3.8 20.0 - - - +
560A SER 2.8 25.0 + - - +
561A SER* 3.8 5.8 - - - +
563A LEU* 1.3 73.0 - - + +
565A ARG* 1.3 58.5 + - - +
567A ILE* 4.0 1.9 - - - +
568A GLN* 3.1 36.2 + - + +
576A VAL* 5.6 0.9 - - + -
578A GLY 5.6 0.7 - - - -
579A HIS 3.7 29.4 - - - +
580A SER* 3.9 16.2 - - - -
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Residues in contact with ARG 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 SER 2.8 18.4 + - - +
562A GLN* 4.0 3.6 - - - +
564A VAL* 1.3 75.7 - - + +
566A ASP* 1.3 65.1 + - - +
567A ILE 3.2 0.4 - - - -
568A GLN* 3.5 18.3 + - - +
569A LYS* 3.1 30.2 + - + +
580A SER* 5.4 3.8 - - - -
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Residues in contact with ASP 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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542A VAL* 6.1 0.4 - - - -
562A GLN 2.7 23.2 + - - +
563A LEU* 3.5 9.6 - - + +
565A ARG* 1.3 71.3 - - - +
567A ILE* 1.3 60.0 + - + +
569A LYS* 3.3 7.6 + - - +
570A ALA* 3.0 30.2 + - - +
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Residues in contact with ILE 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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479A ILE* 4.0 23.3 - - + -
542A VAL* 4.1 18.6 - - + -
555A ILE* 3.9 28.9 - - + -
557A PRO* 3.5 25.1 - - + -
563A LEU* 2.8 43.5 + - + +
564A VAL 4.0 4.0 - - - +
566A ASP* 1.3 74.1 - - + +
568A GLN* 1.3 67.3 + - - +
569A LYS 3.0 1.7 + - - -
570A ALA* 3.1 5.6 + - - +
571A ALA* 2.9 27.8 + - + +
576A VAL* 4.1 17.0 - - + -
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Residues in contact with GLN 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 VAL* 3.1 34.0 + - + +
565A ARG* 3.5 22.6 - - - +
567A ILE* 1.3 76.3 - - - +
569A LYS* 1.3 61.2 + - + +
571A ALA* 3.7 14.6 - - - +
576A VAL* 4.1 26.4 - - + +
578A GLY 6.3 1.4 - - - -
579A HIS* 5.8 0.8 - - - +
580A SER* 4.8 12.1 + - - +
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Residues in contact with LYS 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 ARG* 3.1 20.4 + - + +
566A ASP* 3.5 6.7 - - - +
567A ILE 3.0 1.0 - - - -
568A GLN* 1.3 77.1 - - + +
570A ALA* 1.3 64.0 + - - +
571A ALA 3.2 6.2 + - - -
572A LYS* 4.4 4.3 + - - +
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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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542A VAL* 4.9 23.1 - - + +
566A ASP 3.0 16.1 + - - +
567A ILE* 3.1 4.2 + - - +
569A LYS* 1.3 75.4 - - - +
571A ALA* 1.3 57.6 + - - +
572A LYS* 3.2 13.1 + - - +
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Residues in contact with ALA 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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555A ILE* 3.9 18.8 - - + -
567A ILE* 2.9 16.8 + - + +
568A GLN 3.7 11.4 - - - +
569A LYS 3.2 2.6 - - - -
570A ALA* 1.3 73.8 - - - +
572A LYS* 1.3 62.9 + - - +
573A GLY 3.8 1.9 + - - -
574A ILE* 3.8 18.9 - - + +
576A VAL* 3.7 24.5 - - + +
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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