Contacts of the helix formed by residues 59 - 73 (chain B) in PDB entry 4KBQ
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 VAL 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B ASN* 3.4 40.2 - - - +
57B PRO 3.4 3.0 - - - -
58B LEU* 1.3 78.6 - - - +
60B ALA* 1.3 64.5 + - - +
61B VAL* 3.3 11.4 + - + +
62B TYR* 3.5 52.6 + - + +
63B TYR* 3.7 8.7 - - - -
89B LEU* 3.8 2.0 - - - -
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Residues in contact with ALA 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LEU 3.9 1.0 + - - -
59B VAL* 1.3 70.9 - - - +
61B VAL* 1.3 65.7 + - + +
63B TYR* 3.1 18.5 + - - +
64B THR* 3.5 10.7 + - - -
86B ALA* 4.0 17.4 - - + +
89B LEU* 3.5 32.6 - - + +
90B ASP* 4.1 16.8 - - + +
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Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS* 4.5 10.1 - - + -
59B VAL* 3.3 8.8 + - + -
60B ALA* 1.3 76.9 - - + +
62B TYR* 1.3 69.2 + - + +
64B THR* 2.8 22.3 + - - +
65B ASN* 3.1 28.9 + - - +
646D ASP* 4.1 27.6 - - + +
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Residues in contact with TYR 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ALA* 3.4 33.9 - - + +
27B GLN* 3.7 9.8 + - - +
30B LYS* 3.7 35.7 - - + -
49B TYR* 4.3 12.5 - + + +
52B ALA* 3.7 27.1 - - + -
53B ILE* 3.8 23.4 - - + +
56B ASN* 3.7 24.9 + - - -
59B VAL* 3.7 40.1 - - + +
60B ALA 3.2 0.4 - - - -
61B VAL* 1.3 79.0 - - + +
63B TYR* 1.3 61.3 + - + +
65B ASN* 3.6 7.5 + - - +
66B ARG* 3.1 23.2 + - - +
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Residues in contact with TYR 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ILE* 3.5 41.4 - - + +
57B PRO* 2.8 33.0 + - - +
59B VAL 3.7 14.4 - - - -
60B ALA* 3.1 13.3 + - - +
62B TYR* 1.3 74.7 - - - +
64B THR* 1.3 55.6 + - - +
66B ARG* 3.1 6.1 + - - -
67B ALA* 2.7 35.7 + - - +
82B ASP* 3.5 30.1 - - - +
85B ARG* 3.7 39.7 - - + -
86B ALA* 4.0 7.6 - - + -
89B LEU* 3.9 15.3 - - + -
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Residues in contact with THR 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ALA 3.5 3.8 + - - +
61B VAL* 2.8 24.6 + - - +
63B TYR* 1.3 73.6 - - - +
65B ASN* 1.3 62.4 + - - +
67B ALA* 3.3 9.3 + - + +
68B LEU* 2.8 28.9 + - - +
82B ASP 5.5 0.2 - - - +
83B CYS* 5.6 1.8 - - - -
86B ALA* 3.7 22.9 - - + -
93B SER* 4.5 5.2 - - - +
95B LYS* 4.7 6.1 - - + -
96B ALA* 3.7 31.2 - - + +
99B PHE* 3.9 15.4 - - + -
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Residues in contact with ASN 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS* 4.4 6.1 - - - +
34B ASN* 3.6 13.3 + - - -
49B TYR* 3.5 24.2 + - + +
61B VAL* 3.1 30.1 + - - +
62B TYR* 3.7 5.6 - - - +
64B THR* 1.3 77.2 + - - +
66B ARG* 1.3 59.0 + - - +
68B LEU* 3.0 21.7 + - - +
69B CYS* 3.0 15.2 + - - -
645D VAL* 3.6 14.5 - - + +
646D ASP* 3.0 41.9 + - - +
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Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ALA* 3.7 37.5 - - + -
49B TYR* 3.9 15.0 - - + -
50B GLY* 3.8 13.5 - - - -
53B ILE* 3.5 29.3 - - + +
62B TYR 3.1 13.3 + - - +
63B TYR* 3.1 8.0 + - - +
65B ASN* 1.3 75.7 - - - +
67B ALA* 1.3 66.4 + - - +
69B CYS* 3.0 14.7 + - - +
70B TYR* 3.0 39.9 + - + -
82B ASP* 2.5 41.0 + - - +
85B ARG* 4.4 9.3 - - - +
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B TYR 2.7 21.1 + - - +
64B THR* 3.5 11.2 - - - +
66B ARG* 1.3 73.6 - - - +
68B LEU* 1.3 55.5 + - - +
70B TYR* 3.4 1.2 + - - -
71B LEU* 3.1 26.3 + - - +
79B ALA* 3.6 27.2 - - - +
82B ASP* 3.7 19.6 + - + -
83B CYS* 4.0 17.7 - - - +
99B PHE* 4.8 5.6 - - + +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PHE* 3.5 28.9 - - + -
64B THR 2.8 13.1 + - - +
65B ASN* 3.0 13.9 + - - +
67B ALA* 1.3 75.6 - - - +
69B CYS* 1.3 60.2 + - - +
71B LEU* 3.6 7.6 + - + +
72B LYS* 2.9 51.7 + - + +
99B PHE* 4.0 29.6 - - + -
643D GLU* 3.9 21.8 - - + +
644D GLU 3.8 20.2 - - - +
645D VAL* 3.6 14.4 - - + -
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Residues in contact with CYS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PHE* 3.9 15.9 - - - -
42B TYR* 4.0 11.3 - - + +
45B ALA* 3.8 10.8 - - - -
46B ALA* 3.7 32.3 - - + -
49B TYR* 3.5 34.5 - - - -
65B ASN 3.0 8.7 + - - -
66B ARG* 3.0 8.6 + - - +
68B LEU* 1.3 77.0 - - - +
70B TYR* 1.3 57.9 + - + +
72B LYS* 3.6 4.6 - - - +
73B MET* 2.8 35.3 + - - +
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Residues in contact with TYR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ALA* 4.6 11.6 - - + +
66B ARG* 3.0 42.9 + - + -
67B ALA 3.7 4.5 - - - +
69B CYS* 1.3 75.8 - - + +
71B LEU* 1.3 60.0 + - - +
72B LYS 3.1 1.6 - - - -
73B MET* 3.2 15.3 + - + +
74B GLN 2.9 5.0 + - - -
75B GLN* 2.6 61.4 + - - +
78B GLN* 3.5 45.4 + - + -
79B ALA* 3.7 15.9 - - - +
82B ASP* 3.6 19.3 - - - -
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ALA 3.1 16.5 + - - +
68B LEU* 4.0 8.7 - - + +
69B CYS 3.6 0.2 - - - -
70B TYR* 1.3 74.1 - - - +
72B LYS* 1.3 58.7 + - + +
74B GLN* 2.8 34.7 + - - +
75B GLN 4.5 2.7 - - - +
76B HIS* 4.9 4.4 + - - +
79B ALA* 3.9 3.9 - - + +
99B PHE* 4.3 29.4 - - + +
102B GLN* 4.5 9.4 - - + -
103B CYS* 3.3 34.8 - - - +
106B GLU* 3.9 26.5 - - - +
643D GLU* 4.4 22.7 - - - +
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Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A GLU* 5.5 4.9 + - - -
37B PHE* 4.7 12.3 - - + -
42B TYR* 4.8 21.5 - - + -
68B LEU* 2.9 38.4 - - + +
69B CYS* 3.6 5.4 - - - +
71B LEU* 1.3 77.9 - - + +
73B MET* 1.3 59.2 + - - +
74B GLN* 2.8 14.2 + - - +
640D PRO 5.5 1.4 + - - -
643D GLU* 3.0 37.7 + - - +
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Residues in contact with MET 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B TYR* 3.8 20.2 - - + +
43B PRO* 3.6 41.3 - - + -
46B ALA* 5.3 1.1 - - - -
69B CYS* 2.8 26.1 + - - +
70B TYR* 3.2 17.0 + - + +
72B LYS* 1.3 73.9 - - - +
74B GLN* 1.3 69.4 + - - +
75B GLN* 3.3 38.3 + - - +
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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