Contacts of the helix formed by residues 97 - 110 (chain B) in PDB entry 2JJ7
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 ASN 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B LYS* 2.8 28.1 + - - +
62B TYR* 3.6 21.5 + - - +
93B HIS* 2.7 44.0 + - - +
94B ILE* 3.2 8.3 + - - +
96B GLU* 1.3 95.3 + - - +
98B PRO* 1.4 66.4 - - - +
99B GLU* 3.2 4.0 - - - -
100B ILE* 3.1 31.3 + - + +
101B GLY 3.6 3.3 + - - -
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Residues in contact with PRO 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PHE* 6.0 2.7 - - + -
17B LYS* 5.1 0.2 - - - +
94B ILE* 3.0 14.8 - - + +
95B LYS 3.7 7.2 - - - +
96B GLU 3.5 8.3 - - - +
97B ASN* 1.4 88.4 - - - +
99B GLU* 1.3 72.8 + - - +
101B GLY* 3.0 17.7 + - - -
102B THR 3.3 8.7 + - - -
161B PRO* 3.5 42.0 - - + +
164B LYS* 4.7 7.4 - - - +
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Residues in contact with GLU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PHE* 6.1 3.8 - - + -
17B LYS* 3.2 60.1 + - + +
18B LYS* 4.1 15.0 - - - +
21B GLY* 3.6 19.7 - - - -
98B PRO* 1.3 89.8 - - - +
100B ILE* 1.3 59.2 + - + +
102B THR* 3.3 5.8 + - - +
103B LEU* 2.9 40.0 + - + +
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LYS* 4.8 2.9 - - - -
58B VAL* 4.1 24.9 - - + +
59B PHE* 4.3 26.0 - - + -
62B TYR* 3.5 43.3 - - + +
63B GLY* 4.3 1.8 - - - +
93B HIS* 4.4 4.3 - - + -
94B ILE* 4.4 2.0 - - + -
97B ASN* 3.1 17.3 + - + +
99B GLU* 1.3 74.4 - - + +
101B GLY* 1.3 60.8 + - - +
103B LEU* 4.5 4.5 - - + -
104B ALA* 2.8 35.3 + - - +
122B PHE* 3.6 38.1 - - + -
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Residues in contact with GLY 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ILE* 3.7 19.7 - - - +
97B ASN 3.6 4.0 + - - -
98B PRO 3.0 9.2 + - - -
100B ILE* 1.3 77.3 - - - +
102B THR* 1.3 56.1 + - - +
105B TYR* 2.8 32.4 + - - +
159B LEU* 3.2 31.6 - - - +
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Residues in contact with THR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PHE* 4.0 11.6 - - + +
146A SER* 4.4 22.7 - - - -
149A HIS* 4.3 10.4 + - - -
20B PHE 5.3 0.4 - - - +
21B GLY 3.9 20.0 - - - +
24B GLY* 5.9 3.1 - - - -
98B PRO 3.3 4.9 + - - -
99B GLU* 3.3 9.9 + - - +
101B GLY* 1.3 75.2 - - - +
103B LEU* 1.3 72.2 + - + +
105B TYR* 3.7 2.3 - - - +
106B GLU* 3.1 28.2 + - + +
159B LEU 3.8 1.4 + - - -
161B PRO* 3.3 28.9 - - - +
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Residues in contact with LEU 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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17B LYS 5.1 0.4 - - - +
20B PHE* 3.4 46.7 - - + +
21B GLY* 4.5 3.8 - - - +
24B GLY* 4.5 11.4 - - - -
25B TYR* 4.6 2.2 - - + +
55B TYR* 4.0 23.9 + - + +
58B VAL* 4.5 17.0 - - + -
59B PHE* 3.8 21.3 - - + -
99B GLU* 2.9 27.3 + - + +
100B ILE* 4.2 4.3 - - + +
102B THR* 1.3 77.7 - - + +
104B ALA* 1.3 65.9 + - - +
106B GLU* 3.4 7.9 + - + +
107B GLU* 3.1 27.0 + - - +
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Residues in contact with ALA 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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59B PHE* 3.8 15.6 - - + -
100B ILE 2.8 22.3 + - - +
101B GLY 4.1 1.3 - - - +
103B LEU* 1.3 69.5 - - - +
105B TYR* 1.3 67.0 + - - +
107B GLU* 3.3 1.4 + - - +
108B ILE* 2.9 30.7 + - + +
122B PHE* 3.6 36.3 - - + -
123B ILE* 4.3 10.5 - - + -
159B LEU* 4.4 3.6 - - + -
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Residues in contact with TYR 105 (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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148A ASN 4.7 0.4 - - - -
149A HIS* 3.5 58.1 - + + +
152A HIS* 3.2 31.6 - - + +
101B GLY 2.8 19.7 + - - +
102B THR 3.7 2.0 - - - +
103B LEU 3.3 0.2 - - - -
104B ALA* 1.3 77.3 - - - +
106B GLU* 1.3 62.0 + - - +
108B ILE* 3.1 5.7 + - - +
109B ILE* 2.9 68.0 + - + +
152B HIS* 3.3 14.5 - + - -
155B THR* 4.0 21.5 - - + -
156B SER* 3.8 22.4 - - - -
159B LEU* 3.8 9.8 - - + +
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Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A SER* 2.7 28.8 + - - +
148A ASN* 4.5 7.1 + - - +
149A HIS 4.4 1.7 + - - -
24B GLY* 6.1 5.2 - - - -
102B THR* 3.1 23.0 + - + +
103B LEU* 3.7 11.9 - - + +
104B ALA 3.3 0.2 - - - -
105B TYR* 1.3 84.6 - - - +
107B GLU* 1.3 58.3 + - + +
109B ILE* 3.5 21.6 - - - +
110B LYS* 2.9 36.8 + - - +
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TYR* 2.5 26.7 + - - +
59B PHE* 4.7 0.7 - - + -
103B LEU 3.1 18.8 + - - +
104B ALA 3.3 0.2 + - - -
106B GLU* 1.3 75.9 - - + +
108B ILE* 1.3 64.5 + - - +
110B LYS 3.6 14.9 - - - +
111B GLU* 3.8 7.8 + - - +
112B SER* 2.7 29.9 + - - -
114B ARG* 2.9 27.7 + - - +
115B LEU* 4.5 14.3 + - + +
118B ILE* 3.6 20.8 - - + +
123B ILE* 3.7 21.1 - - + -
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ALA* 2.9 27.6 + - + +
105B TYR* 3.5 4.0 - - - +
107B GLU* 1.3 80.0 - - - +
109B ILE* 1.3 65.1 + - + +
110B LYS 3.6 0.2 + - - -
111B GLU* 4.7 2.4 + - - +
115B LEU* 6.0 0.4 - - - -
122B PHE* 5.4 0.2 - - + -
123B ILE* 3.8 29.8 - - + -
126B PHE* 4.0 18.8 - - + -
151B ILE* 6.5 0.9 - - + -
155B THR* 3.9 21.8 - - + +
159B LEU* 3.7 25.8 - - + -
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Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ASN* 4.9 13.2 - - + +
152A HIS* 5.9 2.7 - - + +
105B TYR* 2.9 66.2 + - + +
106B GLU* 3.5 25.6 - - - +
108B ILE* 1.3 84.2 - - + +
110B LYS* 1.3 63.9 + - + +
111B GLU 4.0 0.8 + - - -
152B HIS* 4.0 16.2 - - + +
155B THR* 5.6 0.7 - - + -
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Residues in contact with LYS 110 (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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106B GLU* 2.9 22.6 + - - +
107B GLU* 3.6 8.5 - - - +
109B ILE* 1.3 86.3 - - + +
111B GLU* 1.3 71.5 + - - +
112B SER* 3.2 6.9 + - - -
114B ARG* 5.7 0.2 + - - -
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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