Contacts of the helix formed by residues 77 - 95 (chain B) in PDB entry 3K3B
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 LYS 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 3.7 3.8 - - - +
75B SER 3.3 11.2 + - - +
76B THR* 1.3 78.1 - - - +
78B GLN* 1.3 65.9 + - - +
79B ILE* 3.3 21.7 - - + +
80B ASP* 3.3 24.1 + - - +
81B VAL* 3.3 21.8 + - - +
131B PRO* 5.7 2.0 - - + +
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Residues in contact with GLN 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 2.9 28.4 + - - +
77B LYS* 1.3 75.2 - - - +
79B ILE* 1.3 63.1 + - - +
81B VAL* 3.2 9.2 + - - +
82B TYR* 3.1 20.4 + - - +
113B PHE* 2.7 49.6 + - + +
114B THR* 4.1 3.8 - - - +
117B GLY* 3.4 3.0 - - - -
131B PRO 3.2 20.9 + - - +
132B LEU* 2.8 26.2 + - + +
133B ALA 3.1 24.9 + - - +
134B GLY* 3.7 2.2 - - - -
135B ILE* 6.1 0.2 - - - +
138B ARG* 3.5 6.3 + - - +
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Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS* 4.0 25.1 - - + +
78B GLN* 1.3 78.4 - - - +
80B ASP* 1.3 71.2 + - - +
82B TYR* 3.3 5.8 + - + +
83B ARG* 3.0 70.1 + - + +
131B PRO 4.8 0.2 + - - -
138B ARG* 3.6 30.0 - - - +
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Residues in contact with ASP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 4.8 1.8 - - + -
75B SER 5.0 0.5 - - - +
76B THR* 3.9 15.9 - - + -
77B LYS* 3.3 39.1 + - - +
78B GLN 3.2 0.6 - - - -
79B ILE* 1.3 84.9 - - - +
81B VAL* 1.3 64.9 + - - +
83B ARG* 4.0 15.1 + - - +
84B SER* 2.8 35.2 + - - +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 3.6 33.2 - - + +
72B PHE* 4.6 14.1 - - + -
76B THR* 3.7 12.6 - - + -
77B LYS 3.4 13.9 - - - +
78B GLN* 3.2 8.9 + - - +
80B ASP* 1.3 77.7 - - - +
82B TYR* 1.3 57.7 + - - +
85B VAL* 2.9 37.0 + - + +
86B VAL* 4.1 0.2 - - - +
114B THR* 4.1 23.3 - - + -
135B ILE* 4.2 15.3 - - + -
333B ILE* 4.2 11.0 - - + -
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Residues in contact with TYR 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLN 3.1 12.3 + - - +
79B ILE* 3.5 11.0 - - + +
80B ASP 3.3 0.2 - - - -
81B VAL* 1.3 77.8 - - - +
83B ARG* 1.3 63.1 + - + +
86B VAL* 2.8 61.1 + - + +
87B CYS* 2.9 38.4 + - - -
90B LEU* 3.2 16.9 - - + +
135B ILE* 4.6 5.8 - - + +
138B ARG* 3.6 31.6 - - + +
139B THR* 3.5 20.8 - - - -
142B GLN* 3.0 43.1 - - + +
146B LYS* 5.3 0.2 - - - +
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Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ILE* 3.0 56.4 + - + +
80B ASP* 4.0 17.1 + - - +
82B TYR* 1.3 79.1 - - + +
84B SER* 1.3 63.5 + - - +
87B CYS* 3.6 30.9 - - - +
88B PRO* 3.9 4.0 - - - +
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Residues in contact with SER 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B MET* 3.7 32.8 - - - +
72B PHE* 3.7 18.7 - - - -
80B ASP* 2.8 23.2 + - - +
83B ARG* 1.3 81.4 - - - +
85B VAL* 1.3 60.4 + - - +
88B PRO* 3.8 12.6 - - - +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL* 4.2 15.5 - - + -
70B MET* 4.4 5.4 - - + -
72B PHE* 3.7 31.9 - - + -
81B VAL* 2.9 23.2 + - + +
84B SER* 1.3 78.0 - - - +
86B VAL* 1.3 69.3 + - + +
88B PRO* 3.4 9.6 - - - +
89B ILE* 3.3 19.6 - - + +
101B ILE* 4.6 4.7 - - + -
331B SER* 3.3 31.0 - - - +
333B ILE* 4.3 13.7 - - + -
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Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL 4.1 2.0 - - - +
82B TYR* 2.8 44.1 + - + +
85B VAL* 1.3 71.9 - - + +
87B CYS* 1.3 64.9 + - - +
88B PRO 3.3 2.0 - - - -
89B ILE* 2.8 5.5 + - - -
90B LEU* 2.7 28.8 + - + +
101B ILE* 4.2 20.9 - - + -
135B ILE* 3.7 38.4 - - + -
139B THR* 3.4 26.5 - - + +
261B LEU* 5.1 2.7 - - + -
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Residues in contact with CYS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 2.9 40.5 + - - -
83B ARG* 3.6 24.0 - - - +
86B VAL* 1.3 72.5 - - - +
88B PRO* 1.4 68.1 - - + +
90B LEU* 3.3 6.4 + - - +
91B ASP* 3.1 32.1 + - - +
142B GLN* 6.1 1.1 - - - -
146B LYS* 5.6 2.0 - - - +
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Residues in contact with PRO 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ARG 3.9 7.9 - - - +
84B SER 3.8 13.2 - - - +
85B VAL 3.4 14.1 - - - +
86B VAL 3.3 5.4 - - - -
87B CYS* 1.4 94.6 - - + +
89B ILE* 1.3 59.1 + - + +
91B ASP* 3.5 12.0 + - + +
92B GLU* 3.3 24.9 + - - +
329B ARG* 3.1 30.8 + - - +
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Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLN* 6.5 0.7 - - + -
85B VAL 3.3 19.5 - - - +
86B VAL* 2.8 8.8 + - + +
88B PRO* 1.3 76.9 - - + +
90B LEU* 1.3 58.7 + - - +
92B GLU* 3.2 8.2 + - - +
93B VAL* 3.0 26.0 + - - +
99B CYS* 3.5 25.6 - - + -
100B THR 4.6 1.1 - - - +
101B ILE* 3.7 18.8 - - + -
261B LEU* 3.6 19.5 - - + -
329B ARG* 3.9 24.2 - - + +
330B THR 5.0 0.2 - - - -
331B SER* 3.5 34.5 - - - +
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 3.2 26.5 - - - +
86B VAL* 2.7 25.4 + - + +
87B CYS* 3.8 5.4 - - - +
89B ILE* 1.3 70.8 - - - +
91B ASP* 1.3 62.2 + - - +
93B VAL* 3.5 14.5 + - + -
94B ILE* 3.0 41.8 + - + +
139B THR* 3.9 20.2 - - + +
142B GLN* 3.7 16.6 - - + -
143B ILE* 3.7 27.4 - - + +
146B LYS* 3.9 16.2 - - + -
261B LEU* 4.8 5.4 - - + -
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Residues in contact with ASP 91 (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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87B CYS* 3.1 23.2 + - - +
88B PRO* 3.5 12.4 - - + +
89B ILE 3.2 0.2 - - - -
90B LEU* 1.3 77.8 - - - +
92B GLU* 1.3 61.4 + - + +
94B ILE* 3.4 7.5 + - - +
95B MET* 3.1 31.6 + - - +
146B LYS* 3.6 26.7 + - - -
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Residues in contact with GLU 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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88B PRO 3.3 5.7 + - - +
89B ILE 3.2 10.2 + - - +
91B ASP* 1.3 75.6 - - - +
93B VAL* 1.3 65.8 + - - +
95B MET* 3.1 24.5 + - - +
97B TYR* 3.3 47.3 + - - +
99B CYS* 3.7 11.9 - - - -
327B ARG 5.7 0.7 - - - -
328B THR* 4.6 8.3 - - - +
329B ARG* 3.2 47.1 + - + +
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Residues in contact with VAL 93 (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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89B ILE 3.0 19.0 + - - +
90B LEU* 3.7 15.0 - - + +
92B GLU* 1.3 74.7 - - - +
94B ILE* 1.3 57.4 + - - +
96B GLY 2.9 16.1 + - - -
97B TYR 3.3 8.4 + - - -
99B CYS* 3.7 18.4 - - + -
243B ILE* 3.7 27.8 - - + -
245B MET* 3.7 0.3 - - - +
259B GLY* 3.1 20.1 - - - -
260B LYS 3.5 38.1 - - - +
261B LEU* 3.8 19.7 - - + -
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Residues in contact with ILE 94 (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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90B LEU* 3.0 39.6 + - + +
91B ASP* 3.8 5.6 - - - +
92B GLU 3.2 0.2 - - - -
93B VAL* 1.3 70.3 - - - +
95B MET* 1.3 58.6 + - + +
96B GLY 3.0 6.7 + - - -
143B ILE* 5.1 3.8 - - - -
146B LYS* 3.2 37.5 - - + +
147B LEU* 3.6 39.5 - - + -
150B ASN* 5.3 5.2 - - - +
243B ILE* 4.7 6.7 - - + -
245B MET* 3.1 22.5 - - - +
257B LYS* 3.0 23.7 + - - +
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Residues in contact with MET 95 (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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91B ASP* 3.1 21.1 + - - +
92B GLU* 3.1 26.5 + - - +
94B ILE* 1.3 77.5 - - + +
96B GLY* 1.3 59.2 + - - +
97B TYR* 3.7 21.6 - - + -
257B LYS* 3.5 20.3 - - - +
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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
------------------------------------------------------------
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