Contacts of the helix formed by residues 83 - 100 (chain B) in PDB entry 5JKC
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 MET 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A TRP* 3.8 33.7 - - + +
150A LYS* 4.5 3.1 - - - +
151A ASN* 3.2 23.8 - - - +
153A LYS* 3.6 22.4 - - + -
155A GLU* 3.2 30.1 - - - +
81B LEU 4.0 0.4 + - - -
82B LEU* 1.3 74.2 - - - +
84B PRO* 1.3 72.4 - - + +
85B GLY* 4.5 2.5 - - - +
86B CYS* 3.0 11.0 + - + +
87B ARG 2.9 17.7 + - - -
142B ASP 4.9 4.7 - - - +
145B MET* 4.3 7.4 - - + -
146B SER* 3.4 28.8 + - - +
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Residues in contact with PRO 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TRP* 3.6 27.4 - - + -
155A GLU* 3.4 29.4 - - + +
156A VAL 3.4 26.2 - - - +
157A HIS* 4.6 6.1 - - + +
82B LEU 4.3 1.1 - - - +
83B MET* 1.3 82.6 - - + +
85B GLY* 1.3 50.7 + - - +
87B ARG* 2.9 12.4 + - + +
88B LYS* 2.8 36.4 + - - +
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Residues in contact with GLY 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLU* 4.1 8.4 + - - -
83B MET* 3.3 2.3 - - - +
84B PRO* 1.3 79.6 - - - +
86B CYS* 1.3 60.8 + - - +
88B LYS* 3.4 16.4 - - - +
89B HIS* 3.2 22.8 - - - -
142B ASP* 4.4 11.0 - - - -
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Residues in contact with CYS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 4.1 8.5 - - + -
83B MET* 3.0 9.2 + - + +
85B GLY* 1.3 72.4 - - - +
87B ARG* 1.3 69.9 + - - +
89B HIS* 3.0 14.3 + - - +
90B PHE* 3.3 31.9 + - - -
142B ASP 3.7 13.1 + - - +
143B CYS* 2.0 52.0 - - - -
146B SER* 3.3 28.9 - - - +
175B PHE* 4.2 1.3 - - - -
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Residues in contact with ARG 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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157A HIS* 3.5 19.7 + - - -
158A ALA* 2.7 42.2 + - - +
160A ARG* 4.0 14.2 - - - +
65B HIS 2.9 26.5 + - - -
66B LEU 4.6 0.6 - - - -
67B ASP* 2.9 30.5 + - - +
76B LEU* 5.1 13.5 - - + -
77B PHE* 6.1 1.8 - - - -
81B LEU* 6.2 2.2 - - - -
82B LEU* 4.2 24.0 - - + +
83B MET 2.9 11.4 + - - +
84B PRO* 2.9 13.2 + - + +
86B CYS* 1.3 75.3 - - - +
88B LYS* 1.3 65.2 + - - +
90B PHE* 3.0 6.8 + - - +
91B ILE* 3.0 34.8 + - + +
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Residues in contact with LYS 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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46B GLU* 3.6 35.3 + - - +
84B PRO 2.8 11.6 + - - +
85B GLY* 3.4 15.5 - - - +
87B ARG* 1.3 77.5 - - - +
89B HIS* 1.3 63.7 + - + +
91B ILE* 3.2 10.6 + - - +
92B GLN* 3.0 41.6 + - - +
210B TRP* 6.1 2.3 - - - -
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Residues in contact with HIS 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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85B GLY 3.2 22.4 + - - -
86B CYS* 3.0 7.7 + - - +
88B LYS* 1.3 79.9 - - + +
90B PHE* 1.3 58.9 + - - +
92B GLN* 3.3 10.0 + - - +
93B ALA* 3.0 23.7 + - - +
135B ASP 4.9 1.3 - - - -
138B GLU* 3.5 14.0 + - + -
139B TRP* 3.4 53.2 - - + +
142B ASP* 2.6 38.4 + - + -
209B LYS* 3.1 33.2 + - - +
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Residues in contact with PHE 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 4.1 25.6 - - + -
82B LEU* 4.0 12.8 - - + -
86B CYS* 3.3 43.8 + - - -
87B ARG 3.0 7.2 + - - +
89B HIS* 1.3 76.4 - - - +
91B ILE* 1.3 65.3 + - - +
93B ALA* 3.2 7.6 + - - +
94B ILE* 3.1 28.2 + - + +
139B TRP* 3.6 30.1 - + - -
143B CYS* 3.7 5.8 - - - -
153B TRP* 3.7 28.0 - + - -
175B PHE* 3.7 23.1 - + - -
185B LEU* 4.3 4.9 - - + -
189B THR* 4.1 9.6 - - + -
190B TRP* 4.7 9.7 - + - -
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Residues in contact with ILE 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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160A ARG* 4.0 19.3 - - - +
46B GLU* 3.9 11.9 - - + -
64B ALA 3.9 15.5 - - - +
65B HIS* 3.6 50.9 - - + +
76B LEU* 5.8 3.6 - - + -
87B ARG* 3.0 39.4 + - + +
88B LYS* 3.7 9.9 - - - +
90B PHE* 1.3 74.7 - - + +
92B GLN* 1.3 57.4 + - - +
94B ILE* 3.0 11.6 + - + +
95B CYS* 2.8 32.9 + - - -
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Residues in contact with GLN 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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46B GLU* 2.9 30.0 + - + +
88B LYS* 3.0 36.3 + - - +
89B HIS* 3.5 12.0 + - - +
91B ILE* 1.3 74.0 - - - +
93B ALA* 1.3 66.5 + - - +
95B CYS* 3.2 7.7 + - - +
96B PHE* 3.0 25.5 + - - +
209B LYS* 3.0 29.8 + - - +
210B TRP* 3.2 50.5 - - + +
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Residues in contact with ALA 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 HIS 3.0 13.5 + - - +
90B PHE 3.3 10.1 - - - +
91B ILE 3.2 0.2 - - - -
92B GLN* 1.3 78.1 - - - +
94B ILE* 1.3 56.1 + - - +
96B PHE* 3.4 5.1 - - - +
97B TYR* 3.0 28.6 + - - +
139B TRP* 3.8 26.9 - - + -
190B TRP* 3.8 18.7 - - + +
194B PHE* 4.3 10.3 - - + -
209B LYS* 3.9 13.2 - - + +
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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
----------------------------------------------------------
64B ALA* 3.4 42.8 - - + +
69B SER* 5.4 4.7 - - - -
71B LEU* 4.0 7.0 - - + -
72B TYR* 3.8 30.1 - - + +
76B LEU* 5.6 7.9 - - + -
90B PHE* 3.1 17.2 + - + +
91B ILE* 3.0 10.6 + - + +
93B ALA* 1.3 73.9 - - - +
95B CYS* 1.3 59.1 + - - +
97B TYR* 3.2 0.7 + - - +
98B GLU* 2.8 38.1 + - + +
190B TRP* 3.6 23.6 - - + -
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Residues in contact with CYS 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU* 3.5 11.9 - - - +
47B CYS* 2.0 60.3 - - - -
50B TRP* 3.7 18.8 - - + -
64B ALA* 4.7 1.6 - - - -
65B HIS* 4.1 7.9 - - - -
91B ILE* 2.8 19.8 + - - +
92B GLN* 3.2 8.9 + - - +
94B ILE* 1.3 71.1 - - - +
96B PHE* 1.3 53.3 + - - +
98B GLU* 4.8 0.9 - - - -
99B CYS* 2.6 44.2 + - - +
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Residues in contact with PHE 96 (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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50B TRP* 3.8 17.8 - + - -
92B GLN 3.0 16.3 + - - +
93B ALA 3.4 2.9 - - - +
95B CYS* 1.3 76.0 - - - +
97B TYR* 1.3 61.9 + - - +
100B SER* 3.0 51.1 + - - -
103B LEU* 3.7 20.7 - - + +
129B VAL* 4.4 4.9 - - + -
131B LEU* 3.7 20.6 - - + -
194B PHE* 3.8 28.7 - + - -
207B LEU* 4.1 16.8 - - + -
208B GLN 3.7 20.2 - - - -
209B LYS* 3.5 24.7 - - + +
219B ASN* 3.8 11.9 - - - -
302B CL 4.5 0.7 - - + -
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Residues in contact with TYR 97 (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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28B MET* 3.5 44.1 - - + +
30B ALA* 5.3 3.5 - - + +
33B HIS* 3.0 25.8 + + - -
72B TYR* 3.9 16.8 - + - +
93B ALA 3.0 17.1 + - - +
94B ILE 3.7 3.8 - - - +
96B PHE* 1.3 79.3 - - - +
98B GLU* 1.3 67.1 + - - +
100B SER 4.7 1.2 + - - +
103B LEU* 4.1 11.6 - - + +
124B GLU 4.8 0.5 + - - -
125B ARG* 4.1 15.9 - - - +
126B VAL* 4.2 16.8 + - + -
190B TRP* 3.4 35.2 - + + -
193B SER* 4.0 18.8 + - - -
194B PHE* 4.8 7.9 - + + -
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Residues in contact with GLU 98 (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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32B HIS* 3.5 35.0 - - - +
33B HIS* 3.5 23.2 + - - -
47B CYS* 6.2 0.4 - - - -
55B CYS* 3.2 30.2 - - - +
56B CYS* 3.5 2.8 + - + +
60B THR* 3.9 25.8 - - + +
64B ALA* 6.2 0.7 - - + -
71B LEU* 4.3 3.3 - - + +
72B TYR* 2.5 37.3 + - - +
94B ILE* 2.8 28.6 + - + +
95B CYS* 4.0 2.5 - - - +
97B TYR* 1.3 81.6 - - - +
99B CYS* 1.3 61.0 + - - +
100B SER 5.5 0.2 - - - -
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Residues in contact with CYS 99 (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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47B CYS* 3.9 26.9 - - - -
50B TRP* 3.6 24.2 - - + -
54B ALA* 3.5 4.5 - - - -
55B CYS 2.9 22.5 + - - +
56B CYS* 2.0 48.2 - - - -
95B CYS* 2.6 27.5 + - - +
98B GLU* 1.3 75.9 - - - +
100B SER* 1.3 62.1 + - - +
101B PRO* 3.4 6.6 - - - +
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Residues in contact with SER 100 (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 ILE 4.4 2.1 - - - +
27B CYS* 5.4 0.2 - - - -
50B TRP* 3.9 5.7 - - - -
55B CYS* 3.4 12.5 - - - +
96B PHE* 3.0 27.6 + - - -
97B TYR 4.7 1.3 + - - +
98B GLU 3.8 0.6 - - - -
99B CYS* 1.3 75.0 - - - +
101B PRO* 1.4 64.3 - - - +
102B ASN* 3.1 13.6 + - - +
103B LEU* 3.5 32.9 + - - +
207B LEU* 5.2 0.2 - - - +
302B CL 3.0 24.8 - - - +
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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
------------------------------------------------------------
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