Contacts of the helix formed by residues 63 - 77 (chain B) in PDB entry 4JCQ
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 HIS 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B GLU* 3.7 23.3 + - - -
30B ILE* 2.7 25.3 + - - +
31B ASN* 4.0 10.7 - - + +
32B GLN* 5.5 1.1 - - + +
62B GLY* 1.3 72.9 - - - -
64B VAL* 1.3 66.5 + - - +
65B GLU* 3.4 25.6 - - - +
66B ALA* 3.2 9.9 + - + +
67B GLY* 3.1 17.5 + - - -
92B ALA* 4.3 2.2 - - - +
121B GLY 3.8 3.4 - - - -
122B VAL 3.2 24.6 + - - -
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLY 3.8 1.2 + - - -
63B HIS* 1.3 70.9 - - - +
65B GLU* 1.3 69.1 + - + +
67B GLY* 3.1 2.8 + - - +
68B ASP* 2.8 47.7 + - - +
92B ALA* 4.9 8.3 - - - -
117B GLN* 6.1 0.2 - - - +
118B PRO* 6.3 0.2 - - + -
120B GLY 5.0 0.7 - - - +
121B GLY* 3.2 26.9 + - - +
139B MET* 3.9 26.5 - - + -
142B ARG* 3.8 14.1 - - - +
143B ILE* 3.8 20.6 - - + -
112C ARG* 4.6 6.7 - - - +
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Residues in contact with GLU 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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32B GLN* 4.4 13.5 - - + +
63B HIS* 3.4 27.8 - - - +
64B VAL* 1.3 91.6 + - + +
66B ALA* 1.3 59.1 + - - +
68B ASP* 3.5 10.2 + - - -
69B THR* 3.1 21.0 + - - -
121B GLY 5.0 0.7 - - - +
58C ASN* 3.2 17.7 + - - +
87C GLY* 3.5 13.5 - - - +
88C TRP* 3.4 66.9 - - + +
112C ARG* 5.8 1.6 - - - +
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Residues in contact with ALA 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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30B ILE* 3.8 8.1 - - + +
31B ASN* 3.4 40.6 - - - +
32B GLN* 3.8 6.7 - - + +
35B ALA* 3.9 9.4 - - + +
63B HIS* 3.2 13.8 + - + +
65B GLU* 1.3 78.1 - - - +
67B GLY* 1.3 64.7 + - - +
69B THR* 3.4 2.8 + - - -
70B ILE* 3.2 28.9 + - - +
58C ASN* 4.3 5.4 - - - +
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Residues in contact with GLY 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 3.5 14.9 - - - +
63B HIS 3.1 12.1 + - - -
64B VAL 3.1 4.2 + - - -
66B ALA* 1.3 75.0 - - - +
68B ASP* 1.3 59.2 + - - +
70B ILE 3.5 0.5 + - - -
71B HIS* 2.9 30.9 + - - +
92B ALA* 4.6 9.4 - - - -
95B THR* 4.7 6.4 - - - +
96B ILE* 3.7 17.3 - - - +
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL* 2.8 27.7 + - - +
65B GLU* 3.6 10.9 - - - +
67B GLY* 1.3 77.4 - - - +
69B THR* 1.3 56.2 + - - +
71B HIS* 3.6 5.5 - - - +
72B ASP* 3.0 35.8 + - - +
95B THR* 4.4 13.0 - - - +
142B ARG* 2.8 45.2 + - - -
143B ILE* 5.2 1.2 - - - +
146B LEU* 5.3 0.2 - - - +
86C THR* 4.7 0.4 - - - -
87C GLY* 4.1 5.4 - - - +
110C ASN* 3.4 25.7 - - + +
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Residues in contact with THR 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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35B ALA* 4.5 4.0 - - + -
39B SER* 4.0 7.2 - - - +
65B GLU 3.1 4.6 + - - -
66B ALA* 3.7 7.4 - - - -
67B GLY 3.3 0.2 - - - -
68B ASP* 1.3 73.8 - - - +
70B ILE* 1.3 59.7 + - - +
72B ASP* 3.3 1.7 + - - +
73B MET* 2.8 37.7 + - + +
27C TYR* 3.3 39.7 - - + +
58C ASN* 2.6 30.2 + - - -
86C THR* 2.8 30.1 + - + +
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Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 3.9 14.6 - - + -
30B ILE* 4.2 5.6 - - + -
34B LEU* 3.7 30.1 - - + -
35B ALA* 3.8 24.0 - - + +
38B VAL* 4.0 17.9 - - + -
39B SER* 5.5 0.9 - - - +
66B ALA 3.2 17.9 + - - +
68B ASP 3.4 0.2 - - - -
69B THR* 1.3 73.0 - - + +
71B HIS* 1.3 66.5 + - - +
73B MET* 3.3 6.7 + - - +
74B ILE* 3.0 29.8 + - + +
96B ILE* 3.7 43.7 - - + -
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Residues in contact with HIS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLY 2.9 19.0 + - - +
68B ASP* 3.6 7.4 - - - +
70B ILE* 1.3 79.0 - - - +
72B ASP* 1.3 86.1 + - - +
74B ILE* 3.4 2.1 + - - -
75B LYS* 3.4 45.0 + - + +
95B THR* 3.1 33.4 - - + +
96B ILE* 4.3 3.7 - - - +
98B LEU 4.6 1.2 + - - -
99B ALA* 3.5 37.1 + - + +
146B LEU* 3.7 27.5 - - + +
110C ASN* 3.5 15.3 + - - -
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Residues in contact with ASP 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASP 3.0 18.7 + - - +
69B THR 3.9 1.8 - - - +
71B HIS* 1.3 95.5 + - - +
73B MET* 1.3 59.9 + - - +
75B LYS* 3.3 7.3 + - - +
76B PHE* 2.8 31.3 + - - +
86C THR* 4.7 1.4 + - - +
108C LEU* 3.4 32.2 - - + +
109C PRO* 3.8 12.3 - - + +
110C ASN* 2.8 45.9 + - - +
184C GLU 4.6 1.2 - - - +
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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
----------------------------------------------------------
39B SER* 3.7 27.1 - - - +
42B LEU* 4.2 15.9 - - + -
43B LEU* 3.9 38.6 - - + -
69B THR* 2.8 30.8 + - + +
70B ILE* 3.3 5.6 + - - +
72B ASP* 1.3 73.4 - - - +
74B ILE* 1.3 66.2 + - - +
76B PHE* 4.0 14.6 - - + -
77B ILE* 3.2 36.3 + - + +
27C TYR* 4.7 2.5 - - - -
56C PHE* 3.8 30.1 - - + -
108C LEU* 4.1 11.0 - - + -
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 4.1 11.9 - - + -
55B ILE* 3.9 28.3 - - + -
70B ILE* 3.0 22.2 + - + +
71B HIS 3.5 7.0 - - - +
73B MET* 1.3 79.4 - - - +
75B LYS* 1.3 61.0 + - - +
77B ILE* 3.5 17.5 - - - +
79B PRO 4.8 1.0 - - - +
81B VAL* 3.8 31.1 - - + +
83B VAL* 5.2 3.6 - - + -
96B ILE* 3.9 37.5 - - + +
99B ALA* 3.7 25.4 - - + +
100B ALA* 4.4 1.6 - - - +
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Residues in contact with LYS 75 (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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71B HIS* 3.4 37.0 + - + +
72B ASP* 3.3 9.9 + - - +
73B MET 3.3 0.2 - - - -
74B ILE* 1.3 74.9 - - - +
76B PHE* 1.3 62.1 + - - +
77B ILE 3.8 4.4 - - - +
98B LEU 4.9 3.0 + - - -
99B ALA* 3.3 28.7 - - - +
101B GLU* 4.8 12.0 + - - +
149B GLU* 5.3 7.1 + - - -
184C GLU* 3.6 34.4 + - + +
185C ASN* 3.0 25.9 + - - +
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Residues in contact with PHE 76 (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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72B ASP 2.8 18.1 + - - +
73B MET* 3.3 26.0 + - + +
75B LYS* 1.3 77.6 - - - +
77B ILE* 1.3 68.6 + - + +
56C PHE* 3.8 20.9 - + - -
108C LEU* 3.8 22.7 - - + -
183C ILE* 3.6 19.3 - - + -
184C GLU 3.2 14.1 - - - +
185C ASN* 3.4 27.1 - - - +
186C ARG* 3.2 63.1 + - - +
189C LEU* 3.8 25.4 - - + -
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Residues in contact with ILE 77 (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 LEU* 3.9 32.5 - - + +
43B LEU* 4.6 1.1 - - + -
46B GLU* 3.4 27.8 - - - +
53B ILE* 3.8 29.6 - - + -
73B MET* 3.2 33.4 + - + +
74B ILE 3.5 10.5 - - - +
75B LYS 3.8 7.1 - - - +
76B PHE* 1.3 83.0 - - + +
78B LYS* 1.3 63.5 + - - +
79B PRO* 3.8 13.6 - - + +
81B VAL* 3.9 17.0 - - + -
185C ASN* 5.3 1.6 + - - -
186C ARG* 4.4 0.4 - - - -
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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