Contacts of the helix formed by residues 85 - 104 (chain B) in PDB entry 3CJD
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 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B ASP* 1.3 89.0 + - - +
86B PRO* 1.4 66.5 - - - +
87B ASN 3.3 2.2 - - - -
88B GLU* 3.0 26.7 + - + +
89B ARG* 3.1 19.8 + - + +
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Residues in contact with PRO 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASP* 3.3 12.6 - - + +
85B HIS* 1.4 88.3 - - - +
87B ASN* 1.3 65.7 + - - +
89B ARG* 3.2 8.3 + - + +
90B LEU* 3.1 27.0 + - - +
140B PRO* 3.5 36.4 - - + +
143B LYS* 4.1 22.2 - - + -
144B ILE* 3.7 19.7 - - + +
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Residues in contact with ASN 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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85B HIS 3.3 1.0 - - - -
86B PRO* 1.3 77.4 - - - +
88B GLU* 1.3 62.1 + - - +
90B LEU* 3.4 7.1 + - - +
91B ILE* 3.1 30.5 + - + +
144B ILE* 3.4 26.6 - - - +
192B LEU* 3.0 23.5 + - - +
193B GLU* 4.0 15.7 + - + -
195B VAL* 2.9 28.5 + - - +
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Residues in contact with GLU 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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85B HIS* 3.0 23.5 + - + +
87B ASN* 1.3 77.2 - - - +
89B ARG* 1.3 58.5 + - - +
91B ILE* 3.4 6.1 + - - +
92B ALA* 2.9 38.2 + - + +
189B ARG* 3.3 39.1 + - - -
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Residues in contact with ARG 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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74B VAL 5.4 5.1 + - - -
75B GLY 5.6 2.0 + - - -
76B ALA 4.9 10.5 + - - -
77B VAL* 4.9 10.0 - - - +
85B HIS* 3.1 19.6 + - - +
86B PRO* 3.2 13.9 + - + +
88B GLU* 1.3 78.0 - - - +
90B LEU* 1.3 58.6 + - - +
92B ALA* 3.4 7.6 + - - +
93B MSE 3.0 46.1 + - + +
140B PRO* 4.5 13.0 - - + -
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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
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201A STE 3.9 16.4 - - + +
86B PRO 3.1 13.0 + - - +
87B ASN* 3.6 10.3 - - - +
88B GLU 3.4 0.2 - - - -
89B ARG* 1.3 72.3 - - - +
91B ILE* 1.3 57.3 + - - +
93B MSE 3.5 25.5 + - + +
94B SER* 2.7 38.8 + - - -
137B ILE* 3.9 14.8 - - + +
140B PRO* 3.8 13.2 - - + -
141B LEU* 3.8 15.5 - - + -
144B ILE* 3.5 31.2 - - + -
160B LEU* 4.8 7.0 - - + -
192B LEU* 3.8 18.2 - - + +
195B VAL* 4.8 5.2 - - + -
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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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87B ASN* 3.1 20.8 + - + +
88B GLU* 3.7 11.2 - - - +
90B LEU* 1.3 76.5 - - - +
92B ALA* 1.3 52.2 + - - +
94B SER* 3.3 3.0 + - - -
95B HIS* 2.8 62.8 + - + +
188B ILE* 4.8 0.7 - - + -
189B ARG* 3.5 53.2 - - - +
192B LEU* 3.6 25.6 - - + -
193B GLU* 3.9 22.9 - - + +
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Residues in contact with ALA 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 GLU* 2.9 24.4 + - + +
89B ARG* 3.7 11.0 - - - +
91B ILE* 1.3 76.3 - - - +
93B MSE 1.3 57.8 + - + +
95B HIS* 3.3 9.6 + - - +
96B ALA* 2.9 27.9 + - - +
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Residues in contact with MSE 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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201A STE 3.5 21.8 - - + +
74B VAL* 3.4 41.6 - - + +
89B ARG* 3.0 27.3 + - + +
90B LEU* 3.6 33.9 - - + +
92B ALA* 1.3 75.2 - - + +
94B SER* 1.3 56.9 + - - +
96B ALA* 3.2 10.1 + - - +
97B TYR 3.0 22.7 + - - -
136B TYR* 3.4 33.0 - - - +
137B ILE* 3.8 11.0 - - + -
140B PRO* 4.0 6.1 - - + -
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Residues in contact with SER 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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201A STE 3.2 26.3 - - - +
90B LEU 2.7 22.6 + - - -
91B ILE 3.5 0.9 - - - -
93B MSE 1.3 71.3 - - - +
95B HIS* 1.3 61.5 + - - +
97B TYR* 3.2 7.2 + - - +
98B LEU* 3.0 27.5 + - - +
164B VAL* 3.6 12.5 - - - +
188B ILE* 3.4 32.0 - - - +
192B LEU* 3.3 9.5 - - - +
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Residues in contact with HIS 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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88B GLU* 5.9 0.2 + - - -
91B ILE* 2.8 42.7 + - + +
92B ALA* 3.3 8.6 + - - +
94B SER* 1.3 75.4 - - - +
96B ALA* 1.3 56.1 + - - +
98B LEU* 3.3 7.5 + - + +
99B ALA* 3.0 29.0 + - - +
185B LYS* 2.9 69.7 + - + -
188B ILE* 4.0 12.7 - - + +
189B ARG* 4.5 12.5 + - - -
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Residues in contact with ALA 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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70B LEU* 5.7 0.7 - - - -
73B ALA* 3.8 36.4 - - + +
74B VAL* 4.4 5.4 - - + -
92B ALA 2.9 13.4 + - - +
93B MSE 3.2 12.7 + - - +
95B HIS* 1.3 75.5 - - - +
97B TYR* 1.3 56.8 + - - +
99B ALA* 3.4 7.5 + - - +
100B PHE* 3.0 28.2 + - - +
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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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201A STE 4.0 30.7 - - + -
70B LEU* 4.1 22.7 - - + -
74B VAL* 5.2 0.6 - - - +
93B MSE 3.0 12.8 + - - +
94B SER* 3.2 8.0 + - - +
96B ALA* 1.3 73.1 - - - +
98B LEU* 1.3 64.3 + - - +
100B PHE* 3.3 6.8 + - - +
101B ALA* 3.0 23.2 + - - +
108B TRP* 3.0 31.5 + + - -
112B PHE* 3.2 10.7 - + - -
161B PHE* 3.5 23.0 - + - -
164B VAL* 4.2 17.0 - - + -
165B HIS* 2.7 45.6 + - - -
168B VAL* 4.3 13.2 - - + -
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Residues in contact with LEU 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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94B SER 3.0 12.3 + - - +
95B HIS* 3.5 9.6 - - + +
97B TYR* 1.3 76.4 - - - +
99B ALA* 1.3 64.4 + - - +
101B ALA* 3.3 4.3 + - - +
102B ARG* 3.0 47.6 + - - +
168B VAL* 3.9 34.1 - - + +
172B LEU* 4.1 4.7 - - + -
184B LEU* 3.7 41.1 - - + -
185B LYS* 3.6 33.4 - - + +
188B ILE* 4.2 7.2 - - + -
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Residues in contact with ALA 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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95B HIS 3.0 15.7 + - - +
96B ALA* 3.7 9.0 - - - +
98B LEU* 1.3 78.1 - - - +
100B PHE* 1.3 52.6 + - - +
102B ARG* 3.3 9.2 + - - +
103B GLU* 2.8 58.3 + - - +
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Residues in contact with PHE 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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66B THR* 3.4 36.3 - - + -
69B ARG* 3.6 33.4 - - + -
70B LEU* 3.5 33.7 - - + -
73B ALA* 5.5 6.1 - - + -
96B ALA 3.0 14.0 + - - +
97B TYR* 3.4 9.2 - + - +
99B ALA* 1.3 72.4 - - - +
101B ALA* 1.3 59.8 + - - +
103B GLU* 4.5 2.5 - - - -
104B HIS* 2.7 72.5 + + + -
107B LEU* 4.9 0.9 - - + -
108B TRP* 4.0 28.9 - + + -
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Residues in contact with ALA 101 (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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97B TYR 3.0 10.0 + - - +
98B LEU 3.5 5.6 - - - +
100B PHE* 1.3 79.1 - - - +
102B ARG* 1.3 60.8 + - - +
105B PRO* 3.3 26.0 - - - +
108B TRP* 3.5 40.5 - - + +
168B VAL* 3.7 8.1 - - + -
172B LEU* 3.4 25.5 - - + +
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Residues in contact with ARG 102 (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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98B LEU* 3.0 34.2 + - + +
99B ALA* 3.6 9.9 - - - +
101B ALA* 1.3 78.8 - - - +
103B GLU* 1.3 63.0 + - + +
105B PRO* 3.6 12.5 - - - +
172B LEU* 3.7 27.5 - - + +
181B GLY* 2.9 34.4 + - - -
184B LEU* 3.6 16.2 - - - +
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Residues in contact with GLU 103 (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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99B ALA* 2.8 41.9 + - - +
100B PHE* 4.6 1.2 + - - -
102B ARG* 1.3 76.1 - - + +
104B HIS* 1.3 84.6 + - + +
105B PRO* 3.4 6.1 - - - +
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Residues in contact with HIS 104 (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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69B ARG* 3.4 31.2 + - - -
100B PHE* 2.7 58.3 + + + +
101B ALA 3.9 0.2 - - - -
103B GLU* 1.3 97.5 + - + +
105B PRO* 1.3 59.1 - - - +
106B LYS 3.3 2.6 + - - -
107B LEU* 3.4 10.5 + - + +
108B TRP* 2.9 27.7 + - - +
202B CL 3.4 12.1 - - + -
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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