Contacts of the helix formed by residues 69 - 78 (chain A) in PDB entry 2KBX
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 THR 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ILE 5.1 0.9 - - - +
61A ASN* 6.2 1.3 - - - -
62A VAL 3.7 8.7 - - - +
63A MET* 4.5 14.6 - - + -
68A ASP* 1.3 88.6 + - - +
70A PRO* 1.3 74.4 - - - +
71A LEU* 3.7 8.4 + - - +
72A HIS* 2.4 55.2 + - + -
73A LEU* 3.3 3.3 + - - +
92A ASP* 4.5 11.1 + - - +
95A ALA* 4.3 14.5 + - + +
96A VAL 4.6 6.5 - - - +
97A ASN* 4.8 3.8 - - + -
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Residues in contact with PRO 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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38A LEU* 4.2 18.2 - - + -
39A HIS* 4.6 3.8 - - + +
42A CYS* 3.8 14.1 - - + -
60A ILE* 3.2 36.6 - - + +
62A VAL* 3.3 29.6 - - + +
68A ASP 3.8 2.4 - - - +
69A THR* 1.3 86.6 - - - +
71A LEU* 1.3 52.8 + - - +
73A LEU* 4.2 14.1 - - + -
74A ALA* 2.4 39.5 + - - +
86A LEU* 4.7 6.7 - - + -
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Residues in contact with LEU 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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60A ILE* 3.5 11.7 - - + +
69A THR* 3.0 10.9 - - - +
70A PRO* 1.3 77.3 - - - +
72A HIS* 1.3 67.6 + - + +
74A ALA* 3.4 6.8 - - - +
75A ALA* 3.0 19.2 + - - +
86A LEU* 3.4 26.2 - - + +
87A LEU* 5.2 12.6 - - + -
91A ALA 4.9 0.4 - - - -
92A ASP* 2.7 63.3 - - - +
93A ILE* 3.3 14.6 - - + +
95A ALA 5.7 0.2 - - - +
103A PRO* 4.2 20.0 - - + +
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Residues in contact with HIS 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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68A ASP* 3.3 14.4 + - - +
69A THR* 2.4 49.9 + - + -
71A LEU* 1.3 78.7 - - - +
73A LEU* 1.3 66.6 + - - +
75A ALA* 2.9 3.1 + - - +
76A SER* 2.6 24.8 + - - -
95A ALA 4.6 1.3 + - - -
96A VAL* 4.2 4.7 - - - -
97A ASN* 3.8 16.3 + - + +
101A ASN* 2.6 51.1 + - - -
103A PRO* 4.1 20.6 - - + +
106A TYR* 4.1 24.8 - + + +
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Residues in contact with LEU 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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39A HIS* 3.6 31.9 - - + +
42A CYS* 4.0 12.8 - - - -
43A ARG* 3.7 20.5 - - + +
64A ASN* 4.6 2.2 - - - +
68A ASP* 3.2 37.5 - - + +
69A THR 4.0 5.6 - - - +
70A PRO* 3.1 7.8 + - + +
72A HIS* 1.3 78.3 - - - +
74A ALA* 1.3 64.3 + - - +
76A SER* 2.9 13.0 + - - +
77A HIS* 2.8 24.3 + - - +
56B ARG* 3.5 36.1 - - - +
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Residues in contact with ALA 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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42A CYS* 3.6 16.3 - - - -
70A PRO 2.4 33.7 + - - +
71A LEU 3.4 5.2 - - - +
73A LEU* 1.3 68.0 - - - +
75A ALA* 1.3 63.8 + - - +
77A HIS* 3.0 20.7 + - - +
78A GLY 3.6 3.8 + - - -
79A HIS 4.5 0.7 + - - -
82A ILE* 4.7 9.7 - - + +
83A VAL* 4.0 19.6 - - + +
86A LEU* 4.1 22.7 - - + -
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Residues in contact with ALA 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 LEU 3.0 7.1 + - - +
72A HIS* 2.9 7.3 + - - +
74A ALA* 1.3 75.0 - - - +
76A SER* 1.3 60.2 + - - +
77A HIS 2.9 10.8 + - - -
78A GLY* 3.5 11.5 + - - +
83A VAL* 4.4 14.1 - - + +
103A PRO* 4.1 24.5 - - + +
106A TYR* 4.9 1.6 - - + -
107A ALA* 4.3 19.3 - - + +
110A TRP* 4.9 6.3 - - - +
112A GLN* 5.0 9.0 - - - +
115A VAL* 5.3 6.7 - - + -
119A LEU* 5.4 2.9 - - + -
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Residues in contact with SER 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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43A ARG* 5.9 1.0 - - - +
72A HIS 2.6 21.2 + - - -
73A LEU* 2.9 25.1 + - - +
75A ALA* 1.3 71.7 - - - +
77A HIS* 1.3 60.8 + - - +
106A TYR* 4.9 13.8 - - - +
110A TRP* 3.8 44.6 - - - +
56B ARG* 4.9 13.0 + - - +
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Residues in contact with HIS 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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42A CYS 4.5 8.7 - - - +
43A ARG* 2.4 38.5 + - + +
44A GLU 3.1 15.0 - - - -
45A GLY* 4.0 0.9 - - - -
73A LEU 2.8 9.1 + - - +
74A ALA* 3.1 13.5 - - - +
75A ALA 2.9 2.6 + - - -
76A SER* 1.3 82.5 - - - +
78A GLY* 1.3 57.4 + - - +
79A HIS* 2.9 56.6 + + + +
82A ILE* 5.7 0.9 - - + -
110A TRP* 5.4 6.7 - - - -
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Residues in contact with GLY 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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74A ALA 3.6 1.8 + - - -
75A ALA* 3.5 10.8 + - - -
77A HIS* 1.3 78.9 - - - +
79A HIS* 1.3 68.0 + - - +
80A ARG* 3.3 25.5 + - - -
83A VAL* 5.6 0.9 - - - -
112A GLN* 4.6 17.9 + - - -
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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