Contacts of the helix formed by residues 560 - 567 (chain A) in PDB entry 3A1B
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 VAL 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A EDO 3.3 7.2 + - - +
545A GLU* 3.0 47.2 + - + +
547A LEU* 5.0 8.3 - - + +
558A PHE 3.9 0.8 + - - -
559A CYS* 1.3 73.3 - - - +
561A GLU* 1.3 58.8 + - - +
563A VAL* 3.9 1.1 - - - +
564A ASP* 2.9 45.6 + - - +
572A ALA* 3.9 20.0 - - + -
576A ILE* 5.7 2.0 - - + -
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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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6A EDO 3.5 37.9 + - - -
473A LYS* 3.8 43.5 + - + +
476A ARG* 3.2 31.6 + - - +
477A GLU* 5.4 2.2 - - - +
544A ARG* 5.1 2.8 + - - -
559A CYS* 3.2 2.6 - - - -
560A VAL* 1.3 81.1 - - - +
562A CYS* 1.3 59.1 + - - +
564A ASP* 3.9 2.8 - - - +
565A LEU* 2.9 37.8 + - + +
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Residues in contact with CYS 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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2A ZN 2.4 35.0 - - - -
476A ARG* 3.2 39.0 - - - +
537A CYS* 4.2 1.6 - - - -
539A ILE* 3.9 27.3 - - + +
540A CYS* 3.6 6.5 - - - -
558A PHE* 5.9 0.2 - - + -
559A CYS* 3.4 5.9 + - - +
561A GLU* 1.3 78.1 - - - +
563A VAL* 1.3 58.6 + - + +
565A LEU* 4.1 5.6 - - - -
566A LEU* 2.7 36.2 + - + +
567A VAL* 5.1 0.2 - - - +
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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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539A ILE* 5.9 0.9 - - + -
547A LEU* 4.4 8.5 - - + -
558A PHE* 3.8 26.9 - - + +
559A CYS 3.1 19.5 + - - +
560A VAL 3.9 3.4 - - - +
562A CYS* 1.3 76.8 - - + +
564A ASP* 1.3 59.5 + - - +
567A VAL* 2.8 34.2 + - + +
568A GLY 3.1 5.7 + - - -
571A ALA* 3.7 6.1 - - + -
572A ALA* 3.5 33.9 - - + +
584A TYR* 3.3 33.7 - - + +
595A LEU* 6.1 0.4 - - + -
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Residues in contact with ASP 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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560A VAL* 2.9 37.2 + - - +
561A GLU* 4.1 2.9 - - - +
563A VAL* 1.3 72.3 - - - +
565A LEU* 1.3 59.0 + - - +
568A GLY* 2.9 36.0 - - - +
569A PRO* 3.2 11.5 - - + +
570A GLY 3.7 12.2 + - - -
572A ALA* 3.3 29.2 + - - +
573A GLN 4.7 0.3 + - - -
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Residues in contact with LEU 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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476A ARG* 3.6 53.6 - - + +
477A GLU* 3.3 43.7 - - - +
480A VAL* 3.4 55.1 - - + +
484A ARG* 5.5 2.1 - - - -
561A GLU* 2.9 23.8 + - + +
562A CYS* 3.7 2.5 - - - +
564A ASP* 1.3 79.0 - - - +
566A LEU* 1.3 62.4 + - + +
568A GLY* 4.5 2.5 + - - -
594A LEU* 4.7 1.2 - - - +
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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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476A ARG* 4.3 10.5 - - - +
480A VAL* 4.0 23.8 - - + -
490A ILE* 4.6 12.3 - - + -
493A ILE* 6.2 0.9 - - + -
495A ILE* 4.3 13.7 - - + +
539A ILE* 4.0 26.9 - - + -
562A CYS* 2.7 20.8 + - + +
565A LEU* 1.3 78.9 - - + +
567A VAL* 1.3 59.0 + - - +
592A TYR 3.7 0.8 - - - +
593A GLY* 3.6 0.2 - - - -
594A LEU* 2.7 53.8 + - + +
595A LEU* 3.7 32.5 - - + -
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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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484A ARG* 5.8 1.2 + - - -
563A VAL* 2.8 18.9 + - + +
566A LEU* 1.3 73.0 - - - +
568A GLY* 1.3 58.7 + - - +
571A ALA* 3.6 20.9 - - + -
584A TYR* 3.7 28.3 - - + +
592A TYR* 3.7 28.0 - - + +
593A GLY* 3.5 16.1 - - - +
595A LEU* 3.7 28.3 - - + -
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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