Contacts of the helix formed by residues 95 - 107 (chain B) in PDB entry 2JG7
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 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B GLU* 3.3 32.4 + - + +
16B LEU* 4.5 5.4 - - + +
91B ALA 3.5 13.0 + - - +
92B LEU 2.9 8.8 + - - +
94B LYS* 1.3 81.9 - - + +
96B ILE* 1.3 64.7 + - - +
97B LYS 3.2 3.0 + - - -
98B VAL* 3.4 21.6 - - + +
99B LEU* 3.0 24.3 + - + +
204B ILE* 4.1 31.6 - - + -
207B GLU* 6.0 1.6 - - - -
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Residues in contact with ILE 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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92B LEU 3.0 9.4 + - - +
93B ARG* 3.2 23.5 + - + +
94B LYS 3.4 1.9 - - - +
95B LYS* 1.3 76.9 - - - +
97B LYS* 1.3 73.7 + - + +
99B LEU* 4.1 0.5 - - - +
100B GLY* 2.9 27.4 + - - -
115B VAL* 3.9 35.7 - - + +
118B VAL* 3.7 24.6 - - + +
119B GLN* 3.6 28.7 - - - +
122B VAL* 5.1 4.5 - - + -
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Residues in contact with LYS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LYS 5.3 0.4 + - - -
95B LYS 3.3 0.6 - - - -
96B ILE* 1.3 88.8 - - + +
98B VAL* 1.3 61.4 + - + +
100B GLY* 3.4 1.0 + - - -
101B SER* 2.9 32.1 + - - -
111B TYR* 3.6 26.6 - - - +
115B VAL* 4.6 4.3 - - + -
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 3.6 25.6 - - + +
15B GLU* 3.8 33.4 - - + +
16B LEU* 3.6 32.4 - - + +
95B LYS* 3.4 26.7 - - + +
97B LYS* 1.3 78.5 - - + +
99B LEU* 1.3 63.9 + - - +
101B SER* 3.3 9.0 + - - -
102B LEU 2.9 22.2 + - - -
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Residues in contact with LEU 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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16B LEU* 4.0 13.7 - - + -
92B LEU* 3.8 28.7 - - + +
95B LYS* 3.0 18.7 + - + +
96B ILE 4.1 0.2 - - - +
98B VAL* 1.3 76.2 - - - +
100B GLY* 1.3 66.4 + - - +
102B LEU* 3.1 8.9 + - + +
103B VAL* 3.0 25.5 + - - +
118B VAL* 3.9 23.1 - - + -
169B VAL* 4.5 10.8 - - + -
197B THR* 4.8 3.1 - - + -
200B ALA* 4.0 26.5 - - + -
201B VAL* 4.2 21.3 - - + +
204B ILE* 3.9 13.0 - - + -
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Residues in contact with GLY 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ILE 2.9 19.0 + - - -
97B LYS 3.7 1.6 - - - -
99B LEU* 1.3 75.9 - - - +
101B SER* 1.3 56.9 + - - +
103B VAL* 3.3 4.3 + - - +
104B SER* 3.0 27.9 + - - -
111B TYR* 4.5 5.3 - - - +
114B GLY* 3.6 32.9 - - - -
115B VAL* 3.8 4.3 - - - -
118B VAL* 3.9 3.0 - - - +
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Residues in contact with SER 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 3.7 24.9 - - - -
97B LYS 2.9 14.7 + - - -
98B VAL* 3.4 8.5 - - - -
99B LEU 3.2 0.2 - - - -
100B GLY* 1.3 74.7 - - - +
102B LEU* 1.3 57.7 + - - +
104B SER* 3.3 5.3 + - - -
105B LEU* 2.9 29.6 + - - +
111B TYR* 3.3 25.9 - - - -
334B TRP* 3.5 20.8 + - - +
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Residues in contact with LEU 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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12B TRP* 3.8 8.4 - - + -
13B LEU* 3.9 17.9 - - + -
16B LEU* 3.6 24.2 - - + -
18B LEU* 3.7 8.1 - - + -
98B VAL 2.9 13.7 + - - +
99B LEU* 3.1 10.1 + - + +
101B SER* 1.3 74.1 - - - +
103B VAL* 1.3 61.1 + - - +
105B LEU* 3.1 7.3 + - + -
106B GLU* 2.8 45.0 + - + +
196B LEU* 3.7 28.0 - - + +
197B THR* 3.8 13.5 - - - +
200B ALA* 3.6 22.0 - - + -
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Residues in contact with VAL 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 LEU 3.0 16.5 + - - +
100B GLY* 3.6 8.7 - - - +
102B LEU* 1.3 72.5 - - - +
104B SER* 1.3 58.3 + - - +
107B MET* 2.7 38.7 + - + +
109B LYS* 3.6 29.4 - - + -
114B GLY* 4.2 11.4 - - - +
117B GLU* 3.8 12.1 - - - +
118B VAL* 4.9 0.4 - - + -
168B PRO* 3.9 14.4 - - + -
169B VAL* 3.5 31.0 - - + -
197B THR* 4.2 14.6 - - + -
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Residues in contact with SER 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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41B CYS* 5.8 0.3 - - - -
100B GLY 3.0 13.7 + - - -
101B SER* 3.4 11.2 - - - -
103B VAL* 1.3 76.7 - - - +
105B LEU* 1.3 58.6 + - - +
108B GLY* 3.2 24.8 + - - -
109B LYS* 2.9 28.1 + - - +
110B ILE 4.3 0.7 - - - -
111B TYR* 4.0 15.9 - - - +
114B GLY* 4.8 0.8 - - - -
333B PRO* 3.4 31.8 + - - +
334B TRP* 4.2 5.6 + - - +
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Residues in contact with LEU 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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4B LEU* 4.2 4.9 - - + -
10B TYR* 3.7 27.8 - - + +
12B TRP* 3.9 24.5 - - + -
13B LEU* 4.1 15.7 - - + -
41B CYS* 3.5 39.4 - - + -
42B PRO* 3.4 19.9 - - - +
48B ILE* 3.9 29.2 - - + -
101B SER 2.9 19.4 + - - +
102B LEU* 3.7 5.2 - - + +
104B SER* 1.3 76.2 - - - +
106B GLU* 1.3 56.9 + - - +
333B PRO* 5.8 0.2 - - - -
334B TRP* 6.4 0.2 - - + -
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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
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39B SER* 2.6 30.4 + - - +
40B TYR 4.0 3.5 - - - +
42B PRO* 3.6 9.8 - - - +
48B ILE* 4.0 10.3 - - + -
102B LEU* 2.8 25.6 + - + +
105B LEU* 1.3 73.8 - - - +
107B MET* 1.3 61.9 + - - +
193B THR 3.8 7.0 - - - +
194B THR* 3.3 14.2 - - + +
195B PRO* 3.3 7.8 - - - +
196B LEU* 3.0 29.4 + - - +
197B THR* 2.7 43.2 + - - +
344B HIS* 3.4 14.2 - - - -
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Residues in contact with MET 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PRO* 3.4 7.0 - - - +
103B VAL* 2.7 28.3 + - + +
106B GLU* 1.3 75.3 - - - +
108B GLY* 1.3 56.3 + - - +
109B LYS* 3.3 35.2 - - + +
165B PHE* 3.4 42.6 - - + +
166B ASN* 3.9 16.8 - - + +
168B PRO* 4.4 7.4 - - + -
194B THR* 4.6 2.0 - - + -
296B THR* 4.2 11.9 - - + -
299B GLN* 3.6 28.3 - - - +
342B PRO 5.2 0.7 - - - +
344B HIS* 2.8 33.3 + - + +
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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
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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