Contacts of the helix formed by residues 81 - 92 (chain B) in PDB entry 3KG2
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 SER 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B VAL* 2.8 28.7 + - - +
53B ALA 4.1 6.5 + - - -
55B SER* 3.8 11.7 - - - -
58B VAL* 3.9 19.5 - - - +
77B TYR* 3.7 6.1 - - - +
78B ASP* 3.0 17.9 + - - +
80B LYS* 1.3 75.7 - - - +
82B VAL* 1.3 65.4 + - - +
83B ASN 3.2 3.6 - - - -
84B THR* 3.0 22.2 + - - -
85B ILE* 3.3 8.8 + - - +
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 3.5 42.4 - - + -
78B ASP 2.9 20.8 + - - +
79B LYS* 3.6 20.2 - - - +
81B SER* 1.3 78.1 + - - +
83B ASN* 1.3 77.6 + - - +
85B ILE* 3.4 2.8 + - - +
86B THR* 3.1 33.8 + - + +
101B PHE* 4.3 10.1 - - + -
103B THR* 4.3 8.5 - - + -
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Residues in contact with ASN 83 (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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55A SER* 3.6 8.8 + - - +
79A LYS 3.7 6.3 + - - -
80A LYS* 3.1 53.9 + - + +
83A ASN* 4.6 9.7 - - - +
79B LYS 4.9 2.4 + - - -
80B LYS 4.4 3.8 + - - +
81B SER 3.2 0.8 - - - -
82B VAL* 1.3 87.8 - - - +
84B THR* 1.3 66.2 + - - +
86B THR* 3.1 9.5 + - - +
87B SER* 3.1 27.0 + - - -
107B HIS* 5.4 5.5 + - - -
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Residues in contact with THR 84 (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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55A SER* 4.4 8.9 + - - -
83A ASN* 5.8 0.7 - - - +
84A THR* 4.0 15.7 + - + +
55B SER* 4.1 20.7 + - - +
58B VAL* 4.6 8.7 - - + -
59B THR* 3.5 32.4 + - - +
62B PHE* 6.2 1.6 - - + -
80B LYS 4.8 1.1 + - - -
81B SER* 3.0 13.6 + - - -
83B ASN* 1.3 80.6 - - - +
85B ILE* 1.3 63.5 + - + +
88B PHE* 3.0 48.6 + - + +
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Residues in contact with ILE 85 (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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17B LEU* 4.6 8.1 - - + -
58B VAL* 3.5 27.8 - - + -
62B PHE* 4.7 15.3 - - + -
76B PHE 5.2 0.9 - - - +
77B TYR* 4.3 23.3 - - + -
81B SER 3.3 11.3 + - - +
82B VAL 3.4 5.6 + - - +
84B THR* 1.3 78.5 - - + +
86B THR* 1.3 66.8 + - + +
87B SER 3.0 0.2 + - - -
88B PHE* 5.0 2.2 - - - -
89B CYS* 2.9 35.1 + - - +
96B PHE* 3.5 54.7 - - + -
110B VAL* 5.3 2.2 - - + -
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Residues in contact with THR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 5.3 1.3 - - + -
82B VAL* 3.2 20.9 + - + +
83B ASN* 3.1 17.3 + - - -
85B ILE* 1.3 77.6 - - + +
87B SER* 1.3 62.9 + - - +
89B CYS* 4.5 0.5 - - - +
90B GLY* 3.3 17.0 + - - -
103B THR* 3.8 29.4 - - + -
107B HIS* 3.8 36.3 + - + +
108B PRO* 4.7 5.4 - - - +
110B VAL* 4.4 16.4 - - + -
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Residues in contact with SER 87 (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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54A ASN* 2.6 29.2 + - - -
55A SER* 3.3 16.2 + - - -
56A PHE* 2.7 13.3 + - - +
83B ASN 3.1 17.4 + - - -
84B THR 3.7 2.0 - - - -
85B ILE 3.0 0.8 + - - -
86B THR* 1.3 80.0 + - - +
88B PHE* 1.3 65.0 + - - +
90B GLY* 3.2 3.1 + - - -
91B THR* 3.0 26.1 + - - -
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Residues in contact with PHE 88 (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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55A SER* 4.7 1.1 - - - -
56A PHE* 3.3 48.2 - + - -
59A THR* 3.6 33.7 - - + -
59B THR* 3.8 16.4 - - + -
62B PHE* 3.4 37.9 - + + -
63B CYS* 4.2 17.7 - - - -
84B THR* 3.0 47.5 + - + +
85B ILE* 4.1 1.3 - - - +
87B SER* 1.3 76.2 - - - +
89B CYS* 1.3 55.7 + - - +
91B THR 3.1 1.0 + - - -
92B LEU* 2.8 41.8 + - + +
315B CYS* 4.7 1.3 - - - -
316B LEU* 4.5 6.1 - - + -
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Residues in contact with CYS 89 (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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62B PHE* 3.5 27.4 - - - -
85B ILE* 2.9 29.5 + - - +
86B THR 4.5 2.2 - - - +
88B PHE* 1.3 77.6 - - - +
90B GLY* 1.3 56.8 + - - +
93B HIS* 3.2 4.5 + - - -
94B VAL* 3.0 47.6 + - - +
96B PHE* 3.5 29.4 - - + -
109B PHE* 3.3 18.6 - - + +
110B VAL* 4.8 3.4 - - + -
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Residues in contact with GLY 90 (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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86B THR 3.3 11.7 + - - -
87B SER 3.2 6.2 + - - -
88B PHE 3.1 0.8 - - - -
89B CYS* 1.3 79.0 - - - +
91B THR* 1.3 61.9 + - - +
93B HIS* 3.5 18.0 + - - -
108B PRO* 4.5 10.1 + - - -
109B PHE* 4.2 14.4 - - - -
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Residues in contact with THR 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASN* 4.3 9.9 + - - -
56A PHE* 3.4 52.1 - - + +
87B SER 3.0 15.7 + - - -
88B PHE 3.1 3.1 + - - -
90B GLY* 1.3 77.8 - - - +
92B LEU* 1.3 62.5 + - + +
93B HIS* 3.2 5.6 + - - -
320B ALA* 4.5 8.9 - - + +
322B PRO* 3.4 24.8 - - - +
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Residues in contact with LEU 92 (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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56A PHE* 4.3 13.0 - - + -
62B PHE* 3.4 30.1 - - + -
66B PHE* 4.1 23.0 - - + -
88B PHE* 2.8 23.3 + - + +
91B THR* 1.3 78.3 - - + +
93B HIS* 1.3 71.2 + - - +
94B VAL* 3.0 18.8 + - + +
315B CYS* 3.8 36.1 - - + +
320B ALA* 4.3 13.5 - - + -
321B VAL 5.5 5.2 - - - +
322B PRO* 4.5 6.3 - - - +
323B TRP* 3.7 14.9 - - - -
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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