Contacts of the helix formed by residues 1070 - 1074 (chain A) in PDB entry 2XT6
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 LYS1070 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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908A PHE* 3.5 30.4 - - + +
977A PHE* 3.6 27.7 - - + -
1010A PRO* 3.9 12.3 + - + -
1011A HIS* 3.4 15.2 + - - +
1012A GLY 2.9 38.0 + - - +
1014A GLU* 3.5 22.6 + - - +
1016A GLN* 4.7 2.5 - - - +
1020A HIS 3.2 21.1 + - - -
1021A THR* 3.4 7.9 + - - +
1069A PRO* 1.3 78.5 - - - +
1071A SER* 1.3 66.7 + - - +
1072A MET 4.0 0.4 - - - +
1073A LEU* 3.2 29.0 - - - +
1074A ARG* 4.6 4.7 + - - +
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Residues in contact with SER1071 (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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1014A GLU* 3.0 32.1 + - - +
1070A LYS* 1.3 74.0 - - - +
1072A MET* 1.3 63.6 + - - +
1073A LEU 3.0 6.6 + - - -
1074A ARG* 3.2 15.7 + - - +
1075A ASN* 3.5 8.4 + - - +
1118A LYS* 4.7 5.9 + - - +
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Residues in contact with MET1072 (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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878A TRP* 3.6 36.3 - - + +
1014A GLU* 4.3 1.0 + - - -
1042A PRO 4.3 2.5 - - - +
1043A SER* 3.4 25.8 - - - +
1044A THR* 5.0 0.2 - - - -
1069A PRO* 3.4 24.2 - - + -
1070A LYS 3.3 1.4 - - - +
1071A SER* 1.3 78.2 + - - +
1073A LEU* 1.4 62.6 + - - +
1074A ARG 3.2 0.8 + - - -
1075A ASN* 3.5 22.3 + - + +
1078A ALA* 3.9 29.2 - - + +
1117A GLY* 5.5 0.2 - - - -
1118A LYS* 3.7 40.6 - - + -
1121A TYR* 3.8 18.2 - - + -
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Residues in contact with LEU1073 (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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877A ASP* 4.2 22.2 - - - +
878A TRP* 3.6 42.9 + - + -
879A ALA* 4.3 6.8 + - + +
908A PHE* 3.8 29.6 - - + -
910A GLN* 3.8 38.4 - - + +
1069A PRO* 4.0 18.1 - - + +
1070A LYS 3.2 17.5 - - - +
1071A SER 3.0 0.6 - - - -
1072A MET* 1.4 78.3 - - - +
1074A ARG* 1.3 70.2 + - + +
1075A ASN 3.6 2.2 - - - +
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Residues in contact with ARG1074 (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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908A PHE* 2.7 41.1 + - - +
909A THR* 3.2 22.0 + - - -
910A GLN* 4.0 8.1 - - - +
1070A LYS 4.8 3.0 + - - +
1071A SER* 3.2 10.0 + - - +
1073A LEU* 1.3 92.0 - - + +
1075A ASN* 1.4 58.1 + - - +
1076A LYS* 2.8 34.9 + - - +
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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