Contacts of the helix formed by residues 666 - 674 (chain A) in PDB entry 5XJY
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 ARG 666 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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662A GLU 3.6 1.0 + - - -
663A LYS 3.4 8.9 + - - +
664A GLU 3.1 17.5 + - - +
665A ALA* 1.3 79.4 - - - +
667A LEU* 1.3 64.0 + - - +
668A LYS 3.3 1.8 - - - -
669A GLU* 3.4 29.2 - - + +
670A THR* 3.2 24.5 + - - +
981A HIS* 3.7 31.5 - - + +
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Residues in contact with LEU 667 (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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13A LYS* 5.1 12.1 - - + +
17A PHE* 4.6 13.2 - - + -
661A TYR* 5.8 4.7 - - + -
662A GLU* 3.0 36.9 + - + +
665A ALA* 4.4 13.5 - - + +
666A ARG* 1.3 76.0 - - - +
668A LYS* 1.3 61.3 + - - +
670A THR* 3.5 16.6 - - + +
671A MET* 2.9 36.8 + - + +
983A VAL* 4.3 14.4 - - + -
984A LEU 4.4 0.7 - - - +
985A PHE* 4.0 40.2 - - + +
986A ASP 4.8 2.9 - - - +
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Residues in contact with LYS 668 (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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659A ILE* 5.4 5.2 - - + +
662A GLU* 3.2 39.1 + - - +
663A LYS* 4.8 25.2 - - + +
666A ARG 3.3 0.6 - - - -
667A LEU* 1.3 78.1 - - - +
669A GLU* 1.3 71.0 + - - +
671A MET* 3.1 6.7 + - - +
672A ARG* 2.9 43.8 + - - +
678A ASN* 5.0 1.1 - - - -
681A LEU* 4.0 30.0 - - + +
682A TRP* 3.3 38.5 - - + +
685A TRP* 5.7 0.9 - - - +
738A THR* 5.8 1.0 + - - -
843A GLU* 6.2 1.0 - - - +
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Residues in contact with GLU 669 (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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663A LYS* 4.5 17.9 - - - +
666A ARG* 3.4 38.4 + - + +
668A LYS* 1.3 86.3 - - - +
670A THR* 1.3 58.9 + - - +
672A ARG* 3.1 23.9 + - - +
673A ILE* 2.9 31.5 + - + +
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Residues in contact with THR 670 (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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666A ARG 3.2 19.5 + - - +
667A LEU* 3.5 15.9 - - + +
669A GLU* 1.3 77.7 - - - +
671A MET* 1.3 66.5 + - + +
673A ILE* 3.4 14.4 + - - +
674A MET* 3.2 31.5 + - + +
979A PRO* 4.6 19.0 - - - +
981A HIS* 5.2 3.8 - - - +
983A VAL* 3.7 32.0 - - + +
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Residues in contact with MET 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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10A LEU* 4.9 6.1 - - + -
13A LYS* 3.4 33.2 - - + +
667A LEU* 2.9 33.8 + - + +
668A LYS* 3.1 8.5 + - - +
670A THR* 1.3 77.9 - - + +
672A ARG* 1.3 59.8 + - - +
674A MET* 3.0 34.2 + - - +
675A GLY 3.7 0.5 + - - -
676A LEU* 3.7 34.6 + - + +
681A LEU* 3.9 23.1 - - + -
1000A LEU* 5.6 8.7 - - - -
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Residues in contact with ARG 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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668A LYS* 2.9 23.7 + - - +
669A GLU* 3.1 32.0 + - - +
671A MET* 1.3 73.4 - - - +
673A ILE* 1.3 67.6 + - + +
675A GLY* 3.2 12.8 + - - -
676A LEU* 3.8 21.6 + - - +
677A ASP* 5.2 3.3 + - - -
678A ASN* 2.5 45.2 + - - +
681A LEU* 5.5 2.4 - - + +
949A LEU* 5.0 16.8 - - + -
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Residues in contact with ILE 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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669A GLU 2.9 15.7 + - - +
670A THR* 3.5 19.5 - - - +
672A ARG* 1.3 79.7 - - + +
674A MET* 1.3 60.4 + - + +
675A GLY* 3.0 6.6 + - - -
947A THR* 4.9 12.2 - - - +
948A GLY* 4.6 21.1 - - - +
972A ARG 5.5 2.1 - - - +
977A VAL* 3.7 32.5 - - + +
979A PRO* 5.7 9.4 - - + -
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Residues in contact with MET 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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670A THR* 3.2 21.9 + - + +
671A MET* 3.0 26.1 + - - +
673A ILE* 1.3 79.5 - - + +
675A GLY* 1.3 59.9 + - - +
676A LEU* 3.5 9.9 + - + +
972A ARG 5.6 2.7 - - - -
976A GLY* 5.7 5.4 - - - -
977A VAL 4.4 22.9 - - - +
983A VAL* 6.2 3.1 - - + -
997A TYR* 5.2 22.0 - - + +
1000A LEU* 4.5 19.3 - - + +
1001A LYS* 5.7 10.2 - - - -
1045A LEU* 5.6 6.1 - - + +
1046A ALA* 5.8 2.5 - - - -
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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