Contacts of the helix formed by residues 95 - 108 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A GLU* 3.3 31.9 + - + +
16A LEU* 4.5 5.2 - - + +
91A ALA 3.5 13.0 + - - +
92A LEU 3.0 9.0 + - - +
94A LYS* 1.3 82.8 - - + +
96A ILE* 1.3 63.3 + - - +
97A LYS 3.3 2.6 + - - -
98A VAL* 3.4 19.0 - - + +
99A LEU* 3.0 24.3 + - + +
204A ILE* 4.1 31.0 - - + -
207A GLU* 6.0 1.8 - - - -
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Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU 3.0 9.2 + - - +
93A ARG* 3.3 23.6 - - + +
94A LYS 3.4 1.9 + - - +
95A LYS* 1.3 76.7 - - - +
97A LYS* 1.3 74.7 + - + +
99A LEU* 4.2 0.3 - - - +
100A GLY* 2.9 26.5 + - - -
115A VAL* 3.9 36.5 - - + +
118A VAL* 3.7 23.5 - - + +
119A GLN* 3.5 28.7 - - - +
122A VAL* 5.1 4.3 - - + -
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LYS 5.3 0.4 + - - -
95A LYS 3.3 0.6 - - - -
96A ILE* 1.3 85.9 - - + +
98A VAL* 1.3 63.1 + - + +
100A GLY 3.4 0.9 + - - -
101A SER* 2.9 32.2 + - - -
111A TYR* 3.6 26.7 - - + +
115A VAL* 4.6 4.7 - - + -
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TRP* 3.6 25.0 - - + +
15A GLU* 3.7 33.2 - - + +
16A LEU* 3.6 33.2 - - + +
95A LYS* 3.4 26.9 - - + +
97A LYS* 1.3 79.6 - - + +
99A LEU* 1.3 62.4 + - - +
101A SER* 3.3 9.0 + - - -
102A LEU 2.9 23.0 + - - -
334A TRP* 6.5 0.4 - - + -
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.0 15.3 - - + -
92A LEU* 3.8 29.8 - - + +
95A LYS* 3.0 18.6 + - + +
96A ILE 4.2 0.2 - - - +
98A VAL* 1.3 75.2 - - - +
100A GLY* 1.3 65.9 + - - +
102A LEU* 3.2 8.4 + - + +
103A VAL* 3.0 26.0 + - - +
118A VAL* 3.8 23.3 - - + -
169A VAL* 4.5 9.4 - - + -
197A THR* 4.8 3.1 - - + -
200A ALA* 4.0 27.6 - - + -
201A VAL* 4.2 21.3 - - + +
204A ILE* 3.9 12.6 - - + -
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Residues in contact with GLY 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ILE 2.9 19.4 + - - -
97A LYS 3.7 1.1 - - - -
99A LEU* 1.3 77.1 - - - +
101A SER* 1.3 55.5 + - - +
103A VAL* 3.2 5.0 + - - +
104A SER* 3.0 28.3 + - - -
111A TYR* 4.6 4.7 - - - +
114A GLY* 3.6 33.2 - - - -
115A VAL* 3.8 4.5 - - - -
118A VAL* 3.9 2.5 - - - +
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Residues in contact with SER 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TRP* 3.7 13.3 - - - -
97A LYS 2.9 19.3 + - - -
98A VAL* 3.4 9.1 - - - -
99A LEU 3.2 0.2 - - - -
100A GLY* 1.3 76.4 - - - +
102A LEU* 1.3 57.2 + - - +
104A SER* 3.3 4.9 + - - -
105A LEU* 2.9 29.5 + - - +
111A TYR* 3.2 17.3 - - - -
334A TRP* 3.0 43.5 + - - +
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TRP* 3.8 8.2 - - + -
13A LEU* 3.9 18.2 - - + -
16A LEU* 3.6 15.0 - - + -
18A LEU* 3.7 7.9 - - + -
98A VAL 2.9 14.1 + - - +
99A LEU* 3.2 9.8 + - + +
101A SER* 1.3 72.7 - - - +
103A VAL* 1.3 60.4 + - - +
105A LEU* 3.2 7.5 + - + -
106A GLU* 2.8 44.2 + - + +
196A LEU* 3.7 28.0 - - + +
197A THR* 3.8 13.9 - - - +
200A ALA* 3.6 31.2 - - + -
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Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU 3.0 16.6 + - - +
100A GLY* 3.5 8.7 - - - +
102A LEU* 1.3 74.7 - - - +
104A SER* 1.3 57.0 + - - +
107A MET* 2.8 39.9 + - + +
108A GLY 3.6 0.2 + - - -
109A LYS* 3.6 29.2 - - + -
114A GLY* 4.2 11.7 - - - +
117A GLU* 3.9 12.1 - - - +
118A VAL* 4.9 0.7 - - + -
168A PRO* 3.9 14.1 - - + -
169A VAL* 3.5 31.0 - - + -
197A THR* 4.2 14.4 - - + -
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Residues in contact with SER 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLY 3.0 13.0 + - - -
101A SER* 3.4 11.4 - - - -
103A VAL* 1.3 76.9 - - - +
105A LEU* 1.3 56.9 + - - +
108A GLY* 3.2 25.5 + - - -
109A LYS* 2.9 26.6 + - - +
110A ILE 4.3 1.1 - - - -
111A TYR* 3.6 15.4 + - - -
114A GLY* 4.8 0.6 - - - -
333A PRO* 3.2 35.0 + - - +
334A TRP* 3.8 4.5 + - - -
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 4.2 4.9 - - + -
10A TYR* 3.8 27.4 - - + +
12A TRP* 4.0 24.0 - - + -
13A LEU* 4.1 15.5 - - + -
41A CYS* 3.5 38.8 - - + -
42A PRO* 3.4 20.6 - - - +
48A ILE* 3.9 30.1 - - + -
101A SER 2.9 18.0 + - - +
102A LEU* 3.2 6.0 + - + +
104A SER* 1.3 77.6 - - - +
106A GLU* 1.3 57.5 + - - +
333A PRO* 5.2 3.6 - - - -
334A TRP* 5.6 6.2 - - + -
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A SER* 2.5 31.2 + - - +
40A TYR 4.0 3.8 - - - +
42A PRO* 3.6 9.1 - - - +
48A ILE* 4.1 9.6 - - + -
102A LEU* 2.8 25.5 + - + +
105A LEU* 1.3 74.9 - - - +
107A MET* 1.3 60.2 + - - +
193A THR 3.8 5.9 - - - +
194A THR* 3.4 13.7 - - + -
195A PRO* 3.3 8.5 - - - +
196A LEU* 3.1 27.7 + - - +
197A THR* 2.7 43.5 + - - +
344A HIS* 3.4 15.3 - - - -
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Residues in contact with MET 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PRO* 3.5 6.1 - - - +
103A VAL* 2.8 28.3 + - + +
106A GLU* 1.3 76.3 - - + +
108A GLY* 1.3 54.4 + - - +
109A LYS* 3.3 35.0 - - + +
165A PHE* 3.5 43.5 - - + +
166A ASN* 4.0 16.6 - - + +
168A PRO* 4.4 7.2 - - + -
194A THR* 4.6 2.2 - - + -
296A THR* 4.2 12.3 - - + -
299A GLN* 3.6 26.2 - - - +
342A PRO 5.1 0.7 - - - +
344A HIS* 2.8 32.1 + - + +
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Residues in contact with GLY 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PRO* 3.7 15.0 - - - +
103A VAL 3.6 0.2 + - - -
104A SER 3.2 15.8 + - - -
106A GLU 3.8 0.4 - - - -
107A MET* 1.3 81.4 - - - +
109A LYS* 1.3 65.4 + - - +
110A ILE 4.0 0.2 + - - -
299A GLN* 6.0 0.4 - - - -
333A PRO* 4.4 6.4 - - - +
341A GLY* 4.1 6.4 - - - -
342A PRO* 3.4 31.9 - - - +
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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