Contacts of the helix formed by residues 95 - 108 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D GLU* 3.3 30.9 + - + +
16D LEU* 4.5 5.4 - - + +
91D ALA 3.5 12.5 + - - +
92D LEU 3.0 8.8 + - - +
94D LYS* 1.3 82.8 - - + +
96D ILE* 1.3 64.4 + - - +
97D LYS 3.3 2.8 + - - -
98D VAL* 3.4 21.0 - - + +
99D LEU* 3.0 23.3 + - + +
204D ILE* 4.2 32.3 - - + -
207D GLU* 6.0 1.8 - - - -
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Residues in contact with ILE 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D LEU 3.0 9.6 + - - +
93D ARG* 3.2 23.3 + - + +
94D LYS 3.4 2.1 + - - +
95D LYS* 1.3 77.0 - - - +
97D LYS* 1.3 72.6 + - + +
99D LEU* 4.1 0.2 - - - +
100D GLY* 2.9 27.2 + - - -
115D VAL* 3.9 35.6 - - + +
118D VAL* 3.7 24.5 - - + +
119D GLN* 3.6 28.5 - - - +
122D VAL* 5.1 4.7 - - + -
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Residues in contact with LYS 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D LYS 5.3 0.2 + - - -
95D LYS 3.3 0.4 - - - -
96D ILE* 1.3 89.6 - - + +
98D VAL* 1.3 62.5 + - + +
101D SER* 2.9 32.1 + - - -
111D TYR* 3.6 25.6 - - - +
115D VAL* 4.6 4.5 - - + -
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Residues in contact with VAL 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D TRP* 3.6 26.8 - - + +
15D GLU* 3.7 33.7 - - + +
16D LEU* 3.5 33.4 - - + +
95D LYS* 3.4 26.5 - - + +
97D LYS* 1.3 79.3 - - + +
99D LEU* 1.3 62.5 + - - +
101D SER* 3.3 8.7 + - - -
102D LEU 2.9 22.0 + - - -
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Residues in contact with LEU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 4.0 15.3 - - + -
92D LEU* 3.9 29.4 - - + +
95D LYS* 3.0 20.3 + - + +
98D VAL* 1.3 74.5 - - - +
100D GLY* 1.3 65.1 + - - +
102D LEU* 3.2 8.9 + - + +
103D VAL* 3.0 26.5 + - - +
118D VAL* 3.8 24.2 - - + -
169D VAL* 4.5 10.1 - - + -
197D THR* 4.8 2.7 - - + -
200D ALA* 4.0 27.1 - - + -
201D VAL* 4.2 20.4 - - + +
204D ILE* 3.9 13.0 - - + -
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Residues in contact with GLY 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ILE 2.9 19.4 + - - -
97D LYS 3.7 1.3 - - - -
99D LEU* 1.3 75.6 - - - +
101D SER* 1.3 56.9 + - - +
103D VAL* 3.3 5.0 + - - +
104D SER* 3.0 27.4 + - - -
111D TYR* 4.5 4.7 - - - +
114D GLY* 3.6 33.3 - - - -
115D VAL* 3.8 5.4 - - - -
118D VAL* 3.9 2.5 - - - +
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Residues in contact with SER 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D TRP* 3.7 24.6 - - - -
97D LYS 2.9 19.0 + - - -
98D VAL* 3.4 9.4 - - - -
100D GLY* 1.3 74.3 - - - +
102D LEU* 1.3 59.8 + - - +
104D SER* 3.3 5.7 + - - -
105D LEU* 2.9 29.5 + - - +
111D TYR* 3.3 22.9 - - - -
334D TRP* 4.2 15.1 + - - +
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Residues in contact with LEU 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D TRP* 3.8 8.2 - - + -
13D LEU* 3.9 18.2 - - + -
16D LEU* 3.6 14.8 - - + -
18D LEU* 3.7 8.3 - - + -
48D ILE* 5.5 0.2 - - + -
98D VAL 2.9 13.7 + - - +
99D LEU* 3.2 10.3 + - + +
101D SER* 1.3 73.9 - - - +
103D VAL* 1.3 59.4 + - - +
105D LEU* 3.2 7.3 + - + -
106D GLU* 2.8 43.4 + - + +
196D LEU* 3.6 27.8 - - + +
197D THR* 3.8 14.6 - - - +
200D ALA* 3.6 31.2 - - + -
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Residues in contact with VAL 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LEU 3.0 17.7 + - - +
100D GLY* 3.3 9.4 + - - +
102D LEU* 1.3 73.9 - - - +
104D SER* 1.3 56.7 + - - +
107D MET* 2.8 39.2 + - + +
109D LYS* 3.5 27.8 - - + -
114D GLY* 4.2 11.2 - - - +
117D GLU* 3.8 13.7 - - - +
118D VAL* 4.9 0.4 - - + -
168D PRO* 3.9 13.9 - - + -
169D VAL* 3.5 30.7 - - + -
197D THR* 4.2 14.1 - - + -
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Residues in contact with SER 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D CYS* 5.8 0.2 - - - -
100D GLY 3.0 13.9 + - - -
101D SER* 3.4 11.0 - - - -
103D VAL* 1.3 77.3 - - - +
105D LEU* 1.3 58.1 + - - +
108D GLY* 3.1 26.9 + - - -
109D LYS* 2.9 26.5 + - - -
110D ILE 4.3 0.9 - - - -
111D TYR* 3.7 15.6 + - - -
114D GLY* 4.8 0.6 - - - -
333D PRO* 3.5 30.5 + - - +
334D TRP* 4.0 6.4 + - - +
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Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 4.2 5.2 - - + -
10D TYR* 3.8 26.9 - - + +
12D TRP* 4.0 24.7 - - + -
13D LEU* 4.1 14.8 - - + -
41D CYS* 3.5 35.0 - - + -
42D PRO* 3.4 19.6 - - - +
48D ILE* 3.9 29.2 - - + -
101D SER 2.9 17.4 + - - +
102D LEU* 3.7 5.8 - - + +
104D SER* 1.3 78.2 + - - +
106D GLU* 1.3 58.4 + - - +
333D PRO* 5.9 0.7 - - - -
334D TRP* 6.2 2.7 - - + -
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Residues in contact with GLU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D SER* 2.6 29.8 + - - +
40D TYR 3.9 4.2 - - - +
42D PRO* 3.6 9.5 - - - +
48D ILE* 4.0 10.1 - - + -
102D LEU* 2.8 27.0 + - + +
105D LEU* 1.3 72.5 - - - +
107D MET* 1.3 60.0 + - - +
193D THR 3.7 6.4 - - - +
194D THR* 3.3 14.6 - - + +
195D PRO* 3.3 7.3 - - - +
196D LEU* 3.0 29.6 + - - +
197D THR* 2.8 44.1 + - - +
344D HIS* 3.4 15.1 - - - -
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Residues in contact with MET 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PRO* 3.5 6.4 - - - +
103D VAL* 2.8 28.4 + - + +
106D GLU* 1.3 76.5 - - - +
108D GLY* 1.3 54.7 + - - +
109D LYS* 3.3 33.7 - - - +
165D PHE* 3.4 42.2 - - + +
166D ASN* 3.9 17.9 - - + +
168D PRO* 4.4 7.2 - - + -
194D THR* 4.6 2.2 - - + -
197D THR* 6.1 0.2 - - - +
296D THR* 4.2 13.0 - - + -
299D GLN* 3.6 27.4 - - - +
342D PRO 5.2 0.5 - - - +
344D HIS* 2.8 32.3 + - + +
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Residues in contact with GLY 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PRO* 3.7 15.0 - - - -
103D VAL 3.6 0.2 + - - -
104D SER 3.1 16.0 + - - -
106D GLU 3.7 0.4 - - - -
107D MET* 1.3 80.5 - - - +
109D LYS* 1.3 64.9 + - - +
299D GLN* 6.0 0.2 - - - -
333D PRO* 3.7 7.5 - - - +
341D GLY* 4.1 5.4 - - - -
342D PRO* 3.3 34.1 - - - +
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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