Contacts of the helix formed by residues 95 - 108 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15E GLU* 3.2 32.0 + - + +
16E LEU* 4.5 5.4 - - + +
91E ALA 3.5 12.3 + - - +
92E LEU 3.0 8.9 + - - +
94E LYS* 1.3 83.3 - - + +
96E ILE* 1.3 64.0 + - - +
97E LYS 3.2 3.3 + - - -
98E VAL* 3.3 21.1 - - + +
99E LEU* 3.0 23.3 + - + +
204E ILE* 4.1 32.3 - - + -
207E GLU* 6.0 2.0 - - - -
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Residues in contact with ILE 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E LEU 3.0 9.2 + - - +
93E ARG* 3.2 23.8 - - + +
94E LYS 3.4 1.9 + - - +
95E LYS* 1.3 76.7 - - - +
97E LYS* 1.3 74.7 + - + +
99E LEU* 4.2 0.3 - - - +
100E GLY* 2.9 26.7 + - - -
115E VAL* 3.9 34.9 - - + +
118E VAL* 3.8 19.7 - - + +
119E GLN* 3.6 32.1 - - - +
122E VAL* 5.1 4.3 - - + -
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Residues in contact with LYS 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E LYS 5.3 0.4 + - - -
95E LYS 3.2 0.8 + - - -
96E ILE* 1.3 88.1 - - + +
98E VAL* 1.3 64.0 + - + +
100E GLY 3.4 0.7 + - - -
101E SER* 2.9 31.2 + - - -
111E TYR* 3.7 27.3 - - - +
115E VAL* 4.5 4.3 - - + -
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Residues in contact with VAL 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E TRP* 3.6 25.5 - - + +
15E GLU* 3.7 34.8 - - + +
16E LEU* 3.6 32.1 - - + +
95E LYS* 3.3 27.4 - - + +
97E LYS* 1.3 79.3 - - + +
99E LEU* 1.3 62.6 + - - +
101E SER* 3.3 8.4 + - - -
102E LEU 2.9 23.2 + - - -
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Residues in contact with LEU 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E LEU* 4.0 15.3 - - + -
92E LEU* 3.9 28.7 - - + +
95E LYS* 3.0 18.8 + - + +
96E ILE 4.2 0.2 - - - +
98E VAL* 1.3 75.0 - - - +
100E GLY* 1.3 65.9 + - - +
102E LEU* 3.2 8.7 + - + +
103E VAL* 3.0 26.7 + - - +
118E VAL* 3.8 23.3 - - + -
169E VAL* 4.5 10.3 - - + -
197E THR* 4.8 2.7 - - + -
200E ALA* 4.0 26.7 - - + -
201E VAL* 4.2 20.9 - - + +
204E ILE* 3.9 13.7 - - + -
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Residues in contact with GLY 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ILE 2.9 19.2 + - - -
97E LYS 3.7 1.1 - - - -
99E LEU* 1.3 76.9 - - - +
101E SER* 1.3 55.9 + - - +
103E VAL* 3.3 4.1 + - - +
104E SER* 3.0 28.6 + - - -
111E TYR* 4.5 5.1 - - - +
114E GLY* 3.6 32.1 - - - -
115E VAL* 3.8 4.5 - - - -
118E VAL* 3.9 2.3 - - - +
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Residues in contact with SER 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E TRP* 3.7 24.5 - - - -
97E LYS 2.9 16.6 + - - -
98E VAL* 3.4 10.8 - - - -
99E LEU 3.2 0.2 - - - -
100E GLY* 1.3 73.9 - - - +
102E LEU* 1.3 59.3 + - - +
104E SER* 3.3 5.3 + - - -
105E LEU* 2.8 29.8 + - - +
111E TYR* 3.3 24.0 - - - -
334E TRP* 3.6 17.6 + - - +
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Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E TRP* 3.8 8.4 - - + -
13E LEU* 3.9 18.2 - - + -
16E LEU* 3.6 15.0 - - + -
18E LEU* 3.7 7.6 - - + -
48E ILE* 5.5 0.2 - - + -
98E VAL 2.9 14.1 + - - +
99E LEU* 3.2 11.2 + - + +
101E SER* 1.3 73.0 - - - +
103E VAL* 1.3 59.2 + - - +
105E LEU* 4.3 6.5 - - + -
106E GLU* 2.8 44.3 + - + +
196E LEU* 3.6 29.4 - - + +
197E THR* 3.7 14.1 - - - +
200E ALA* 3.6 30.7 - - + -
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Residues in contact with VAL 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E LEU 3.0 17.8 + - - +
100E GLY* 3.6 9.2 - - - +
102E LEU* 1.3 72.4 - - - +
104E SER* 1.3 58.4 + - - +
107E MET* 2.8 39.1 + - + +
108E GLY 3.6 0.2 + - - -
109E LYS* 3.6 28.7 - - + -
114E GLY* 4.2 11.4 - - - +
117E GLU* 3.8 12.8 - - - +
118E VAL* 4.9 0.4 - - + -
168E PRO* 3.9 14.4 - - + -
169E VAL* 3.5 30.7 - - + -
197E THR* 4.2 14.1 - - + -
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Residues in contact with SER 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E GLY 3.0 13.7 + - - -
101E SER* 3.4 10.8 - - - -
103E VAL* 1.3 76.7 - - - +
105E LEU* 1.3 56.6 + - - +
108E GLY* 3.1 27.4 + - - -
109E LYS* 2.9 26.9 + - - +
110E ILE 4.3 1.1 - - - -
111E TYR* 3.6 16.0 + - - +
114E GLY* 4.8 0.6 - - - -
333E PRO* 3.4 31.3 + - - +
334E TRP* 4.2 5.5 + - - +
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Residues in contact with LEU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E LEU* 4.2 5.6 - - + -
10E TYR* 3.8 26.2 - - + +
12E TRP* 4.0 24.0 - - + -
13E LEU* 4.1 15.3 - - + -
41E CYS* 3.5 40.4 - - + -
42E PRO* 3.4 17.5 - - - +
48E ILE* 3.9 29.8 - - + -
101E SER 2.8 19.0 + - - +
102E LEU* 3.2 5.8 + - + +
104E SER* 1.3 75.2 - - - +
106E GLU* 1.3 61.1 + - - +
333E PRO* 5.8 1.3 - - - -
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Residues in contact with GLU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E SER* 2.6 30.8 + - - +
40E TYR 3.9 4.2 - - - +
42E PRO* 3.6 9.8 - - - +
48E ILE* 4.0 11.0 - - + -
102E LEU* 2.8 27.0 + - + +
105E LEU* 1.3 74.6 - - - +
107E MET* 1.3 60.3 + - - +
193E THR 3.8 6.8 - - - +
194E THR* 3.3 15.1 - - + -
195E PRO* 3.3 8.0 - - - +
196E LEU* 3.0 29.8 + - - +
197E THR* 2.8 42.8 + - - +
344E HIS* 3.4 14.4 - - - -
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Residues in contact with MET 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E PRO* 3.4 6.6 - - - +
103E VAL* 2.8 28.1 + - + +
106E GLU* 1.3 74.6 - - - +
108E GLY* 1.3 56.8 + - - +
109E LYS* 3.3 35.7 - - + +
165E PHE* 3.5 43.7 - - + +
166E ASN* 4.0 15.9 - - + +
168E PRO* 4.4 7.0 - - + -
194E THR* 4.6 2.9 - - + -
296E THR* 4.3 12.3 - - + -
299E GLN* 3.7 26.2 - - + +
342E PRO 5.1 0.7 - - - +
344E HIS* 2.8 32.6 + - + +
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Residues in contact with GLY 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E PRO* 3.7 15.0 - - - -
104E SER 3.1 16.9 + - - -
106E GLU 3.7 0.6 - - - -
107E MET* 1.3 81.4 - - - +
109E LYS* 1.3 65.0 + - - +
110E ILE 4.0 0.2 + - - -
299E GLN* 6.0 0.2 - - - -
333E PRO* 3.8 8.4 - - - +
341E GLY* 4.1 5.5 - - - -
342E PRO* 3.4 33.8 - - - +
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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
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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