Contacts of the helix formed by residues 648 - 657 (chain A) in PDB entry 1O94
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 CYS 648 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487A THR* 4.6 1.8 - - - -
646A SER* 3.3 19.1 + - - -
647A GLU* 1.3 75.6 + - - +
649A THR* 1.3 59.2 + - - +
650A LEU 3.4 2.9 - - - +
651A TRP* 3.4 22.5 - - + +
652A ASN* 2.9 47.0 + - - -
671A LEU* 4.7 2.2 - - + -
675A ALA* 3.7 18.6 - - + +
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Residues in contact with THR 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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647A GLU* 3.2 17.8 + - - -
648A CYS* 1.3 77.0 - - - +
650A LEU* 1.3 58.6 + - - +
652A ASN* 3.1 11.0 + - - +
653A GLU* 2.9 54.9 + - + +
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Residues in contact with LEU 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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395A VAL* 3.9 28.5 - - + -
470A MET* 3.8 22.2 - - + +
471A THR* 3.6 6.3 - - - +
472A ALA* 3.5 35.0 - - + +
475A VAL* 4.4 3.1 - - + -
485A ILE* 4.1 17.3 - - + -
487A THR* 4.4 14.1 - - + +
647A GLU* 4.6 1.2 + - - -
648A CYS 3.4 0.4 - - - -
649A THR* 1.3 77.6 - - - +
651A TRP* 1.3 63.9 + - - +
653A GLU* 3.2 9.2 + - - +
654A LEU* 3.0 30.1 + - + +
1731A ADP 4.0 8.7 - - - +
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Residues in contact with TRP 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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485A ILE* 4.2 14.2 - - + +
648A CYS* 3.4 17.6 + - + +
650A LEU* 1.3 77.9 - - - +
652A ASN* 1.3 80.7 + - - +
654A LEU* 3.1 8.5 + - + +
655A LYS* 2.9 72.2 + - + +
669A ILE* 3.3 47.8 - - + -
670A TYR 4.0 0.9 - - - -
671A LEU* 3.7 60.6 - - + +
701A GLN* 4.3 8.5 - - + -
137B LYS* 4.5 20.3 - - - +
140B ASP* 5.1 2.3 + - - -
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Residues in contact with ASN 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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648A CYS* 2.9 35.1 + - - +
649A THR* 3.1 9.0 + - - +
651A TRP* 1.3 93.7 + - - +
653A GLU* 1.3 59.5 + - + +
655A LYS* 3.4 5.4 + - - +
656A ALA* 2.9 30.5 + - - +
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Residues in contact with GLU 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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471A THR* 5.7 1.0 - - - -
472A ALA* 3.9 26.2 + - + +
649A THR* 2.9 38.8 + - + +
650A LEU* 3.2 10.2 + - - +
652A ASN* 1.3 79.5 - - + +
654A LEU* 1.3 61.0 + - - +
656A ALA* 3.5 9.3 + - - +
657A ARG* 3.4 26.9 + - - +
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Residues in contact with LEU 654 (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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472A ALA* 3.6 34.5 - - + +
475A VAL* 3.8 20.9 - - + -
476A LEU* 3.9 21.5 - - + -
485A ILE* 3.7 32.5 - - + -
650A LEU* 3.0 26.0 + - + +
651A TRP* 3.6 6.5 - - - +
653A GLU* 1.3 72.8 - - - +
655A LYS* 1.3 65.2 + - + +
657A ARG* 3.2 4.9 + - - +
658A GLU 3.1 7.4 + - - -
661A TRP* 2.9 33.8 + - + -
669A ILE* 4.3 12.3 - - + -
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Residues in contact with LYS 655 (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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651A TRP* 2.9 68.0 + - + +
652A ASN* 3.9 6.3 - - - +
654A LEU* 1.3 72.2 - - - +
656A ALA* 1.3 57.4 + - - +
657A ARG 3.0 5.2 - - - -
658A GLU* 2.9 49.2 + - - +
661A TRP* 3.8 21.2 - - + -
669A ILE 5.4 0.6 + - - -
140B ASP* 3.6 23.6 + - - +
142B SER* 5.4 4.4 + - - -
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Residues in contact with ALA 656 (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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652A ASN 2.9 18.6 + - - +
653A GLU* 3.6 9.9 - - - +
655A LYS* 1.3 74.4 - - - +
657A ARG* 1.3 63.0 + - + +
658A GLU 3.5 0.6 + - - -
659A SER* 5.5 0.7 + - - -
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Residues in contact with ARG 657 (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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472A ALA* 4.1 14.1 - - - +
473A ASP* 2.8 41.8 + - - -
476A LEU* 3.6 20.7 - - + +
653A GLU* 3.4 17.0 + - - +
654A LEU* 3.2 8.9 + - - +
655A LYS 3.0 0.8 - - - -
656A ALA* 1.3 82.4 - - + +
658A GLU* 1.3 65.7 + - - +
659A SER* 3.0 7.6 - - - +
660A GLU* 2.9 58.4 + - + +
661A TRP* 3.4 8.5 - - - -
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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