Contacts of the helix formed by residues 670 - 674 (chain A) in PDB entry 6DBU
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 670 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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667A LYS* 3.1 49.8 + - - +
669A ASN* 1.3 76.5 - - - +
671A GLU* 1.3 70.6 + - - +
672A LEU* 2.9 17.5 + - - +
673A SER 3.0 18.7 + - - +
674A CYS* 4.9 0.6 - - - +
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Residues in contact with GLU 671 (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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669A ASN 3.2 5.2 + - - -
670A SER* 1.3 83.2 + - - +
672A LEU* 1.3 68.8 + - + +
673A SER 3.0 2.2 + - - -
674A CYS* 3.4 22.2 + - + +
982A GLY 4.1 5.4 - - - +
985A SER* 2.7 33.7 + - - +
986A GLY* 3.9 20.9 - - - +
988A LYS* 4.6 9.2 + - - -
989A LEU* 4.0 28.9 - - + +
1013A HIS* 5.3 1.6 - - - -
1016A TYR* 5.1 7.4 + - - +
1017A THR* 4.4 4.2 + - - -
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Residues in contact with LEU 672 (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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492A ASN* 5.4 1.8 - - - +
667A LYS* 3.2 31.4 - - + +
670A SER* 2.9 9.5 + - - +
671A GLU* 1.3 83.7 - - + +
673A SER* 1.3 57.4 + - - +
674A CYS 3.8 0.4 - - - -
1016A TYR* 3.6 35.9 - - + +
1017A THR* 3.2 18.3 + - - -
1019A LYS* 5.3 0.8 + - - +
1022A GLN* 3.0 44.8 + - + +
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Residues in contact with SER 673 (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 THR* 3.2 32.3 + - - +
646A ILE 4.9 1.6 + - - -
665A GLU* 3.8 25.0 + - - +
667A LYS* 4.8 3.8 - - - +
668A PRO 4.8 5.4 - - - +
669A ASN 5.7 0.2 - - - -
670A SER 3.0 12.5 + - - +
671A GLU 3.0 0.4 - - - -
672A LEU* 1.3 77.3 - - - +
674A CYS* 1.3 60.1 + - - +
675A ARG* 4.2 8.8 - - - +
1017A THR* 3.8 4.0 - - - -
1019A LYS* 3.9 15.5 + - - -
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Residues in contact with CYS 674 (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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616A LYS* 6.1 2.7 - - - -
618A SER* 5.3 2.9 - - - -
641A ARG* 5.5 2.2 + - - +
643A SER* 3.2 32.4 - - - -
645A THR* 3.2 13.5 - - - -
670A SER 4.9 0.2 - - - +
671A GLU* 3.4 21.5 + - + +
673A SER* 1.3 77.7 - - - +
675A ARG* 1.3 62.5 + - - +
676A PRO* 3.3 9.7 - - - +
982A GLY* 4.4 3.4 - - - -
983A ASN* 3.8 28.9 - - - +
986A GLY* 6.2 1.6 - - - -
1013A HIS* 4.3 10.2 + - - -
1017A THR* 3.5 7.2 + - - -
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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