Contacts of the helix formed by residues 69 - 79 (chain A) in PDB entry 2KJD
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 GLN 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A GLN* 3.7 3.6 - - - -
67A GLY 5.4 2.0 - - - +
68A LYS* 1.3 79.0 - - - +
70A HIS* 1.3 66.2 + - - +
71A GLY 3.3 3.6 - - - +
72A ASP* 3.2 23.0 + - - +
73A VAL* 3.2 24.8 + - - +
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Residues in contact with HIS 70 (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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26A LEU* 5.3 14.6 - - + -
28A SER* 2.7 30.8 + - - +
35A GLN* 3.2 17.7 + - - +
69A GLN* 1.3 74.3 - - - +
71A GLY* 1.3 67.3 + - - +
73A VAL* 3.5 1.0 + - - +
74A VAL* 3.0 51.7 + - + +
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Residues in contact with GLY 71 (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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69A GLN* 3.3 3.4 - - - +
70A HIS* 1.3 83.7 - - - +
72A ASP* 1.3 58.4 + - - +
74A VAL* 4.7 2.0 - - - -
75A SER* 2.8 35.2 + - - -
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Residues in contact with ASP 72 (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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65A MET* 4.1 6.7 - - + +
68A LYS* 3.9 20.2 - - + +
69A GLN* 3.2 47.1 + - - +
71A GLY* 1.3 77.1 - - - +
73A VAL* 1.3 62.1 + - - +
75A SER* 4.0 3.3 - - - -
76A ALA* 3.1 23.9 + - - +
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Residues in contact with VAL 73 (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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26A LEU* 5.3 0.2 - - + -
34A GLY* 6.0 1.1 - - - -
35A GLN* 3.8 33.9 - - + +
57A ILE* 4.1 23.1 - - + -
60A VAL* 4.5 3.1 - - + -
65A MET* 3.7 33.7 - - + +
68A LYS* 4.1 8.3 - - + +
69A GLN 3.2 16.7 + - - +
70A HIS 4.0 1.1 - - - +
72A ASP* 1.3 73.7 - - - +
74A VAL* 1.3 65.0 + - - +
76A ALA* 3.2 8.3 + - - +
77A ILE* 3.0 37.4 + - + +
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Residues in contact with VAL 74 (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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26A LEU* 4.7 17.3 - - + -
35A GLN* 5.6 1.6 - - + -
70A HIS* 3.0 48.4 + - + +
71A GLY* 4.2 2.9 - - - +
73A VAL* 1.3 77.7 - - + +
75A SER* 1.3 62.7 + - - +
77A ILE* 3.1 12.6 + - + +
78A ARG* 3.0 44.8 + - + +
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Residues in contact with SER 75 (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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71A GLY 2.8 20.9 + - - -
72A ASP* 4.0 4.0 - - - -
74A VAL* 1.3 77.7 - - - +
76A ALA* 1.3 57.3 + - - +
78A ARG* 3.3 12.9 + - - +
79A ALA* 2.9 30.9 + - - +
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Residues in contact with ALA 76 (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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60A VAL* 3.9 11.4 - - + +
61A ASN* 2.9 20.9 + - - +
63A VAL* 5.9 1.1 - - + -
65A MET* 3.6 23.8 - - + -
72A ASP 3.1 15.3 + - - +
73A VAL 3.2 9.8 + - - +
75A SER* 1.3 74.9 - - - +
77A ILE* 1.3 62.2 + - - +
79A ALA* 3.2 15.5 + - - +
80A GLY 3.2 2.1 + - - -
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Residues in contact with ILE 77 (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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22A TYR* 4.7 14.8 + - + -
24A PHE* 4.9 14.4 - - + -
26A LEU* 4.1 24.5 - - + -
57A ILE* 5.9 0.4 - - + -
60A VAL* 3.6 23.1 - - + -
61A ASN* 4.0 2.1 + - - +
73A VAL* 3.0 24.2 + - + +
74A VAL* 3.1 16.8 + - + +
76A ALA* 1.3 76.4 - - - +
78A ARG* 1.3 58.8 + - + +
80A GLY* 3.0 19.1 + - - -
81A GLY 4.3 3.3 + - - +
83A GLU 5.0 0.3 - - - +
84A THR* 3.8 28.9 - - + +
86A LEU* 4.3 11.7 - - + -
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Residues in contact with ARG 78 (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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22A TYR* 6.4 1.1 - - - -
74A VAL* 3.0 34.2 + - + +
75A SER* 3.7 9.6 + - - +
77A ILE* 1.3 78.9 - - + +
79A ALA* 1.3 56.7 + - - +
80A GLY 3.1 3.2 + - - -
81A GLY* 3.6 13.5 + - - +
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Residues in contact with ALA 79 (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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61A ASN* 4.5 0.4 - - - -
75A SER* 2.9 18.5 + - - +
76A ALA* 3.2 10.7 + - - +
77A ILE 3.2 0.2 - - - -
78A ARG* 1.3 74.2 - - - +
80A GLY* 1.3 61.5 + - - +
81A GLY 3.3 1.8 - - - -
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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