Contacts of the helix formed by residues 645 - 653 (chain A) in PDB entry 1B0K
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 GLU 645 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A THR* 4.7 5.0 - - + +
78A MET* 3.6 19.2 - - - +
79A ALA 4.0 0.5 + - - -
82A GLN* 2.8 32.4 + - - -
182A GLY* 5.1 1.2 - - - -
183A GLY* 3.4 23.7 - - - +
184A ALA* 3.2 14.2 + - - +
643A SER 3.1 4.9 + - - -
644A ARG* 1.3 68.1 - - - +
646A HIS* 1.3 76.2 + - + +
647A SER 3.2 0.7 - - - -
648A ALA* 2.9 15.7 + - + +
649A LEU* 3.0 23.6 + - + +
671A ASN* 3.8 26.8 + - + +
675A GLN* 3.8 11.5 - - - +
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Residues in contact with HIS 646 (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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74A ALA 4.4 7.2 - - - -
75A THR* 4.9 6.7 - - + -
78A MET* 3.7 36.8 - - + +
571A SER* 4.1 7.9 - - - +
580A ARG* 3.2 58.1 + - - +
583A LEU* 5.9 0.9 - - + -
586A ILE* 4.4 14.4 - - + -
644A ARG* 3.0 12.5 + - + +
645A GLU* 1.3 87.4 + - + +
647A SER* 1.4 57.2 + - - +
649A LEU* 4.2 10.8 - - + -
650A GLU* 2.8 52.7 + - + +
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Residues in contact with SER 647 (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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567A THR* 3.5 25.5 - - - +
570A ILE* 3.8 25.2 - - - +
571A SER* 3.7 18.1 - - - -
644A ARG* 3.4 9.6 + - - +
645A GLU 3.2 0.8 - - - -
646A HIS* 1.4 75.4 - - - +
648A ALA* 1.3 57.2 + - - +
650A GLU* 5.0 1.1 - - - -
651A PRO* 3.2 21.2 - - - +
668A HIS* 3.6 28.3 + - - -
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Residues in contact with ALA 648 (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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645A GLU* 2.9 8.8 + - - +
647A SER* 1.3 79.2 - - - +
649A LEU* 1.3 60.8 + - - +
650A GLU 3.3 1.3 - - - -
651A PRO* 3.9 2.6 - - - +
652A ARG* 3.6 5.7 + - - +
668A HIS* 4.1 2.6 - - + -
671A ASN* 3.7 38.8 - - + +
672A LEU* 3.8 22.9 - - + +
675A GLN* 4.1 6.6 - - + +
677A LEU* 3.2 23.0 - - - +
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Residues in contact with LEU 649 (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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78A MET* 3.7 42.0 - - + -
82A GLN* 4.8 7.9 - - - +
541A LEU* 5.4 6.7 - - + -
544A PHE* 4.2 16.8 - - + -
583A LEU* 3.9 20.7 - - + +
645A GLU* 3.0 25.7 + - + +
646A HIS* 4.0 9.9 - - + +
648A ALA* 1.3 73.5 - - - +
650A GLU* 1.3 62.4 + - - +
652A ARG* 3.1 7.6 + - - +
653A HIS* 2.9 27.7 + - - +
675A GLN* 3.4 39.3 - - - +
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Residues in contact with GLU 650 (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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571A SER* 2.8 27.5 + - - -
583A LEU* 4.6 2.9 - - + -
586A ILE* 3.5 27.5 - - + +
587A SER* 3.6 23.8 - - - +
589A ASN* 2.7 26.4 + - - -
590A LEU* 3.5 21.8 + - + +
646A HIS* 2.8 28.4 + - - +
647A SER* 5.1 0.2 - - - -
649A LEU* 1.3 79.0 - - - +
651A PRO* 1.4 64.1 - - + +
653A HIS* 3.3 3.5 + - - +
654A LEU* 3.2 26.0 + - - +
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Residues in contact with PRO 651 (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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570A ILE* 5.6 1.1 - - + -
590A LEU* 3.5 23.3 - - + -
591A LEU* 6.1 0.7 - - + -
630A TRP* 3.8 27.8 - - + -
647A SER 3.2 27.8 - - - +
648A ALA* 3.9 9.9 - - - +
650A GLU* 1.4 83.0 - - + +
652A ARG* 1.3 56.8 + - - -
654A LEU 3.8 0.3 + - - -
655A GLY 3.6 2.6 + - - -
656A GLY* 2.8 29.0 + - - -
659A ILE* 4.7 14.4 - - + -
672A LEU* 5.0 2.2 - - + -
677A LEU* 4.6 14.6 - - + -
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Residues in contact with ARG 652 (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 PHE* 3.6 34.8 - - + +
545A ASP* 3.1 47.7 + - - -
546A LYS 5.8 0.2 - - - -
648A ALA 3.6 13.5 + - - +
649A LEU* 3.1 11.9 + - - +
651A PRO* 1.3 75.9 - - - +
653A HIS* 1.3 65.2 + - - +
655A GLY* 3.4 11.4 + - - -
656A GLY 4.4 7.9 + - - -
657A ARG* 4.0 19.8 - - - +
675A GLN* 3.1 25.8 + - + +
676A GLY* 4.2 11.5 + - - -
677A LEU* 3.9 18.1 - - + +
742A GLY* 3.2 22.4 + - - -
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Residues in contact with HIS 653 (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 GLN* 5.7 1.6 + - - -
544A PHE* 4.4 8.9 - + - -
583A LEU* 3.8 29.0 + - + +
584A ASP* 2.9 44.3 + - - +
587A SER* 3.0 22.6 + - - +
621A ARG* 4.6 0.4 - - - -
624A LYS* 2.7 37.1 + - - -
649A LEU 2.9 15.1 + - - +
650A GLU 3.7 4.0 - - - +
652A ARG* 1.3 75.9 - - - +
654A LEU* 1.3 67.5 + - + +
655A GLY 3.2 4.2 + - - -
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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