Contacts of the helix formed by residues 104 - 118 (chain A) in PDB entry 3CJR
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 HIS 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PHE* 3.6 24.1 - + + -
101A THR* 5.9 0.2 - - - -
102A GLY* 3.6 1.2 - - - +
103A HIS* 1.3 82.1 - - - +
105A GLU* 1.3 77.8 + - - +
106A THR* 2.7 37.4 + - + -
107A THR* 3.3 8.7 + - - +
108A ARG* 3.1 20.3 + - - +
247A TRP* 3.4 39.1 + + - -
35B MET 5.0 4.5 - - - -
36B GLU* 5.1 10.9 + - + +
39B ALA* 3.4 30.0 - - + +
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Residues in contact with GLU 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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103A HIS 3.7 1.3 + - - +
104A HIS* 1.3 91.5 + - - +
106A THR* 1.3 56.9 - - - +
108A ARG* 3.3 23.0 + - - +
109A LEU* 2.9 35.4 + - - +
244A GLU* 3.7 36.8 - - + +
245A GLY* 5.1 5.1 - - - -
246A GLU 5.5 0.2 + - - -
247A TRP* 3.8 27.5 + - + -
36B GLU* 4.6 15.5 - - - +
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Residues in contact with THR 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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99A PHE* 3.9 5.0 - - - -
104A HIS* 2.7 26.5 + - + +
105A GLU* 1.3 72.9 - - - +
107A THR* 1.3 70.7 + - - +
109A LEU* 3.3 3.9 + - - +
110A ALA* 3.1 18.5 + - - +
191A ASN* 3.0 27.5 + - - -
217A THR* 3.4 19.4 - - - +
218A GLY* 3.6 16.6 - - - +
247A TRP* 3.5 40.8 - - + -
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Residues in contact with THR 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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99A PHE* 3.5 15.2 - - - -
100A GLY* 4.5 1.7 - - - -
102A GLY* 3.8 25.8 + - - +
104A HIS* 3.3 11.3 + - - +
106A THR* 1.3 77.6 + - - +
108A ARG* 1.3 57.6 + - - +
110A ALA* 3.3 5.7 + - - +
111A LEU* 3.0 38.3 + - + +
133A VAL* 3.7 21.8 - - + -
134A LEU* 3.9 4.4 - - + +
191A ASN* 3.6 5.3 + - - +
255A SFG 2.7 31.4 + - - +
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Residues in contact with ARG 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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70A ALA* 4.6 7.5 - - - +
71A LEU 3.6 23.4 + - - +
72A ALA* 3.9 16.7 - - + +
102A GLY 3.2 24.0 - - - +
103A HIS* 2.9 24.7 + - - +
104A HIS 3.1 6.6 + - - +
105A GLU* 3.7 19.6 - - - +
107A THR* 1.3 74.1 - - - +
109A LEU* 1.3 64.3 + - - +
111A LEU* 3.4 4.0 + - + +
112A LYS* 3.1 40.0 + - - +
244A GLU* 2.7 47.3 + - - +
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Residues in contact with LEU 109 (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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105A GLU 2.9 29.2 + - - +
106A THR* 3.6 5.2 - - - +
108A ARG* 1.3 77.1 - - - +
110A ALA* 1.3 56.1 + - - +
112A LYS* 3.5 11.1 + - + +
113A ALA* 3.0 28.8 + - - +
116A ARG* 4.9 2.1 + - - -
217A THR* 4.0 14.4 - - - +
242A ALA* 3.9 23.2 - - + +
243A ALA 3.8 24.0 - - - +
244A GLU* 4.1 15.4 + - + +
247A TRP* 4.0 25.4 - - + +
248A VAL 4.0 9.9 - - - -
249A LEU* 3.6 13.8 - - + +
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Residues in contact with ALA 110 (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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106A THR 3.1 15.7 + - - +
107A THR 3.7 5.2 - - - +
108A ARG 3.3 0.2 - - - -
109A LEU* 1.3 74.1 - - - +
111A LEU* 1.3 61.3 + - - +
113A ALA* 3.7 1.6 - - - +
114A LEU* 2.9 35.1 + - - +
134A LEU* 3.8 27.8 - - + -
189A VAL* 4.0 11.2 - - + +
217A THR* 3.9 14.1 - - + -
249A LEU* 3.6 10.5 - - + +
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Residues in contact with LEU 111 (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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72A ALA* 3.9 21.8 - - + -
75A PHE* 3.4 27.8 - - + -
77A VAL* 4.0 21.8 - - + -
91A LEU* 3.6 15.0 - - + -
107A THR* 3.0 30.7 + - + +
108A ARG* 3.6 9.0 - - + +
109A LEU 3.4 0.2 - - - -
110A ALA* 1.3 77.0 - - - +
112A LYS* 1.3 60.3 + - - +
114A LEU* 3.5 4.8 + - + +
115A ALA* 3.3 15.1 + - - +
133A VAL* 4.4 5.2 - - + +
134A LEU* 3.7 17.0 - - + -
137A ALA* 3.4 32.3 - - + -
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Residues in contact with LYS 112 (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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71A LEU 4.9 2.8 + - - -
72A ALA* 3.9 12.3 - - - +
73A PRO* 3.4 47.7 - - - +
108A ARG* 3.1 26.9 + - - +
109A LEU* 3.8 9.6 - - + +
111A LEU* 1.3 73.6 - - - +
113A ALA* 1.3 64.5 + - - +
115A ALA* 3.2 14.1 + - - +
116A ARG* 3.2 32.8 + - - +
244A GLU* 4.8 11.7 + - - +
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Residues in contact with ALA 113 (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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109A LEU 3.0 18.4 + - - +
110A ALA 3.7 4.5 - - - +
112A LYS* 1.3 74.2 - - - +
114A LEU* 1.3 64.0 + - - +
116A ARG* 3.2 25.0 + - - +
117A HIS* 3.0 34.3 + - + +
215A LEU* 3.8 13.0 - - + -
249A LEU* 3.7 23.3 - - + -
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Residues in contact with LEU 114 (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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110A ALA 2.9 20.1 + - - +
111A LEU* 3.6 7.2 - - - +
112A LYS 3.3 0.2 - - - -
113A ALA* 1.3 77.0 - - - +
115A ALA* 1.3 56.7 + - - +
118A LEU* 2.8 50.5 + - + +
124A VAL* 4.6 4.3 - - + -
134A LEU* 3.6 41.3 - - + +
137A ALA* 4.3 8.7 - - + -
138A ALA* 4.3 9.4 - - + +
141A LEU* 3.9 12.4 - - + +
187A LEU* 3.8 28.3 - - + -
189A VAL* 4.2 16.4 - - + -
215A LEU* 3.9 6.9 - - + +
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Residues in contact with ALA 115 (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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74A PRO* 3.4 38.6 - - + -
111A LEU 3.3 5.5 + - - +
112A LYS* 3.2 10.6 + - - +
114A LEU* 1.3 78.3 - - - +
116A ARG* 1.3 61.7 + - + +
117A HIS 3.7 0.2 + - - -
118A LEU 4.7 5.9 + - - +
119A ARG* 6.0 0.2 + - - -
141A LEU* 3.8 15.0 - - + +
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Residues in contact with ARG 116 (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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109A LEU 4.9 1.2 + - - -
112A LYS* 3.5 31.6 + - - +
113A ALA* 3.2 29.7 + - - +
115A ALA* 1.3 77.7 - - + +
117A HIS* 1.3 66.9 + - + +
118A LEU 5.5 0.2 - - - -
119A ARG* 6.0 0.2 + - - -
240A GLU* 2.8 40.2 + - - +
242A ALA* 4.2 22.9 - - - +
249A LEU* 4.5 2.8 - - - +
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Residues in contact with HIS 117 (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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113A ALA* 3.0 27.9 + - + +
116A ARG* 1.3 86.9 + - + +
118A LEU* 1.3 65.9 + - - +
119A ARG* 3.5 14.4 + - - +
122A ASP* 4.2 2.1 - - - +
187A LEU* 3.8 21.8 - - + +
213A ARG* 3.0 41.7 + - - +
215A LEU* 3.5 21.5 - - + +
239A LEU* 4.3 7.9 - - + -
240A GLU* 2.7 38.2 + - + +
251A ALA* 4.1 13.0 - - + -
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Residues in contact with LEU 118 (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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114A LEU* 2.8 32.6 + - + +
115A ALA 4.7 5.2 - - - +
117A HIS* 1.3 73.3 - - - +
119A ARG* 1.3 75.7 + - - +
120A PRO* 4.2 2.8 - - - +
122A ASP* 3.3 25.8 - - + +
124A VAL* 3.2 27.4 - - + -
138A ALA* 3.6 44.9 - - + +
141A LEU* 4.1 20.5 - - + +
143A GLY* 4.1 4.3 - - - +
187A LEU* 4.0 16.3 - - + +
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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