Contacts of the helix formed by residues 562 - 571 (chain A) in PDB entry 4OSI
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 THR 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 CYS* 3.7 1.8 - - - -
561A LEU* 1.3 72.8 - - - +
563A PRO* 1.3 72.4 - - - +
564A GLN* 2.8 25.4 + - + +
565A GLN* 2.8 36.3 + - + +
566A VAL* 3.1 24.6 + - - +
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Residues in contact with PRO 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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525A HIS 5.0 6.3 - - - +
527A LEU* 3.9 24.5 - - + -
531A GLN* 5.1 1.8 - - - +
552A LEU* 4.1 11.4 - - + -
556A CYS* 3.6 19.0 - - - -
561A LEU 4.2 0.4 - - - +
562A THR* 1.3 86.0 - - - +
564A GLN* 1.3 51.7 + - - +
566A VAL* 3.1 3.1 + - - +
567A VAL* 2.9 40.6 + - - +
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Residues in contact with GLN 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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531A GLN* 4.6 16.0 - - - +
562A THR* 2.8 18.2 + - - +
563A PRO* 1.3 74.9 - - - +
565A GLN* 1.3 57.5 + - - +
567A VAL* 3.6 2.8 + - - +
568A ALA* 3.0 25.8 + - - +
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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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560A GLY 4.7 1.0 - - - +
561A LEU* 3.5 22.0 - - + +
562A THR* 2.8 49.2 + - + +
564A GLN* 1.3 78.1 - - - +
566A VAL* 1.3 67.5 + - - +
568A ALA* 3.1 10.3 + - + +
569A ILE* 2.9 28.4 + - + +
598A GLU* 4.0 28.1 + - - +
601A VAL* 3.9 30.2 - - + +
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Residues in contact with VAL 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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548A VAL* 4.4 18.8 - - + -
552A LEU* 3.6 43.7 - - + +
555A LEU* 4.1 20.4 - - + -
556A CYS* 4.2 6.3 - - - -
561A LEU* 4.4 10.1 - - + -
562A THR 3.1 13.4 + - - +
563A PRO 3.4 7.2 - - - +
565A GLN* 1.3 77.0 - - - +
567A VAL* 1.3 57.2 + - + +
569A ILE* 3.2 10.7 + - - +
570A ALA* 2.9 27.6 + - - +
579A LEU* 4.3 12.3 - - + +
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Residues in contact with VAL 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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527A LEU* 4.2 17.0 - - + -
531A GLN* 3.7 39.3 - - + +
534A ALA* 4.6 2.5 - - + -
535A ILE* 4.0 25.6 - - + -
548A VAL* 5.9 0.2 - - - -
563A PRO 2.9 21.1 + - - +
564A GLN 3.9 4.7 - - - +
566A VAL* 1.3 75.7 - - + +
568A ALA* 1.3 65.0 + - - +
570A ALA* 3.3 5.1 + - - +
571A SER* 3.0 43.1 + - - +
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Residues in contact with ALA 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 GLN* 3.0 18.3 + - - +
565A GLN* 3.1 14.1 + - - +
567A VAL* 1.3 77.4 - - - +
569A ILE* 1.3 60.6 + - - +
571A SER* 3.3 7.5 + - - -
572A HIS* 3.2 23.4 + - - -
601A VAL* 4.9 3.1 - - + -
605A SER* 3.7 16.6 - - - +
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Residues in contact with ILE 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* 5.4 0.7 - - + -
561A LEU* 4.8 7.9 - - + -
565A GLN 2.9 23.0 + - - +
566A VAL* 3.2 6.5 + - - +
568A ALA* 1.3 73.1 - - - +
570A ALA* 1.3 61.4 + - - +
571A SER 3.5 0.3 + - - -
572A HIS* 3.9 10.0 - - - +
575A GLY* 4.1 4.2 - - - -
578A ALA* 3.6 26.9 - - + +
579A LEU* 3.8 24.7 - - + +
582A VAL* 3.9 24.0 - - + -
601A VAL* 3.6 34.1 - - + -
604A ALA* 3.6 29.1 - - + +
605A SER* 3.8 7.9 - - - +
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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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535A ILE* 4.0 20.6 - - + +
538A ASN* 5.4 0.2 - - - +
544A ALA* 4.0 12.4 - - + +
548A VAL* 3.5 32.1 - - + -
566A VAL 2.9 13.5 + - - +
567A VAL* 3.3 4.0 + - - +
569A ILE* 1.3 74.0 - - - +
571A SER* 1.3 53.1 + - - +
572A HIS 2.7 26.7 + - - +
575A GLY* 4.0 11.6 - - - -
579A LEU* 4.2 9.4 - - + +
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Residues in contact with SER 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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534A ALA* 3.8 9.2 - - - +
535A ILE* 3.8 20.9 + - - +
538A ASN* 2.4 24.9 + - - +
567A VAL* 3.0 34.4 + - - +
568A ALA* 3.3 7.1 + - - -
569A ILE 3.3 2.0 - - - -
570A ALA* 1.3 73.6 - - - +
572A HIS* 1.3 71.3 + - - +
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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