Contacts of the helix formed by residues 101 - 113 (chain D) in PDB entry 5JCZ
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 ASN 101 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D ASP* 2.6 43.0 + - - +
97D LEU* 3.1 32.4 + - - +
98D THR 3.6 2.2 + - - +
99D TYR 3.2 0.4 - - - -
100D GLU* 1.3 76.1 - - - +
102D VAL* 1.3 63.3 + - - +
103D GLU 3.2 2.7 - - - -
104D ARG* 3.0 25.7 + - + +
105D TRP* 3.1 19.1 + - - +
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Residues in contact with VAL 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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89D LEU* 3.8 33.2 - - + +
90D VAL 5.0 0.9 - - - +
91D TYR* 4.0 14.4 - - + -
98D THR 3.6 12.7 + - - +
99D TYR* 3.2 27.6 - - + +
100D GLU 3.2 0.8 - - - -
101D ASN* 1.3 77.3 - - - +
103D GLU* 1.3 58.2 + - + +
105D TRP* 3.2 4.4 + - + +
106D LEU* 2.8 28.6 + - + +
121D LEU* 4.0 19.7 - - + -
142D PHE* 3.8 27.4 - - + -
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Residues in contact with GLU 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 TYR 5.7 0.7 - - - +
100D GLU* 3.7 13.6 + - - +
102D VAL* 1.3 78.5 - - + +
104D ARG* 1.3 56.9 + - - +
106D LEU* 3.4 12.5 + - - +
107D LYS* 3.0 28.2 + - - +
142D PHE* 3.6 31.2 - - + -
146D ASN* 5.4 1.4 - - - +
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Residues in contact with ARG 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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19D ASP* 5.4 0.2 - - - -
70D GLN 4.8 4.9 + - - -
71D GLU* 4.2 29.7 + - - +
100D GLU 4.8 0.2 + - - -
101D ASN* 3.0 20.9 + - + +
103D GLU* 1.3 80.0 - - - +
105D TRP* 1.3 99.8 + - - +
107D LYS* 3.3 10.5 + - + +
108D GLU* 3.1 48.4 + - - +
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Residues in contact with TRP 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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17D ILE* 4.0 15.3 - - + +
18D GLY* 3.6 35.2 - - - -
19D ASP* 2.7 33.5 + - - +
69D GLY* 3.6 34.8 - - - -
70D GLN 4.1 5.6 - - - -
72D ARG* 5.0 4.3 - - - -
81D TYR* 4.3 2.0 + - - -
89D LEU* 3.8 15.7 - - + -
90D VAL 5.4 0.7 - - - -
98D THR 5.3 1.6 - - - -
101D ASN 3.1 25.3 + - - -
102D VAL* 3.8 7.4 - - + +
104D ARG* 1.3 108.5 - - - +
106D LEU* 1.3 60.6 + - - +
108D GLU* 3.4 35.6 + - - +
109D LEU* 3.0 27.5 + - - +
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Residues in contact with LEU 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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89D LEU* 4.1 14.5 - - + +
102D VAL 2.8 18.4 + - - +
103D GLU* 3.6 11.0 - - - +
105D TRP* 1.3 77.2 - - - +
107D LYS* 1.3 57.6 + - - +
109D LEU* 3.3 22.5 - - + +
110D ARG* 3.1 50.6 + - + +
119D ILE* 4.1 14.8 - - + -
142D PHE* 4.4 16.2 - - + -
146D ASN* 4.0 31.4 - - + +
148D LEU* 4.5 7.9 - - + -
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Residues in contact with LYS 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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103D GLU 3.0 13.1 + - - +
104D ARG* 3.4 13.2 - - + +
105D TRP 3.1 0.2 - - - -
106D LEU* 1.3 75.4 - - - +
108D GLU* 1.3 63.7 + - - +
109D LEU 3.1 0.2 - - - -
110D ARG* 3.3 6.8 + - - +
111D ASP* 3.1 44.3 + - - +
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Residues in contact with GLU 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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17D ILE* 4.8 0.7 - - - +
70D GLN 5.2 1.4 - - - +
72D ARG* 3.9 15.1 + - - -
77D THR* 3.9 10.0 + - + +
80D TYR* 5.8 0.3 - - - -
81D TYR* 2.4 38.3 + - + +
104D ARG* 3.1 28.6 + - - +
105D TRP* 3.4 35.6 + - - +
107D LYS* 1.3 76.2 - - - +
109D LEU* 1.3 61.7 + - - +
111D ASP* 3.3 9.8 + - - -
112D HIS* 3.1 38.5 + - + +
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Residues in contact with LEU 109 (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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17D ILE* 3.8 19.1 - - + -
81D TYR* 3.4 29.4 + - + -
87D ALA* 4.4 6.5 - - + -
89D LEU* 4.9 0.7 - - + -
105D TRP 3.0 12.8 + - - +
106D LEU* 3.3 18.8 - - + +
108D GLU* 1.3 76.9 - - - +
110D ARG* 1.3 60.3 + - - +
113D ALA* 2.9 56.6 + - + +
117D ILE* 4.1 16.6 - - + -
119D ILE* 3.5 43.3 - - + -
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Residues in contact with ARG 110 (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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106D LEU* 3.1 33.0 + - + +
107D LYS* 3.3 7.8 + - + +
109D LEU* 1.3 78.9 - - - +
111D ASP* 1.3 65.2 + - - +
112D HIS 3.5 0.3 + - - -
113D ALA 4.3 8.6 - - - +
114D ASP 5.0 1.2 + - - -
115D SER* 4.2 20.4 + - - +
117D ILE* 4.5 9.9 + - - +
119D ILE* 3.6 32.3 - - - +
146D ASN* 4.3 15.6 + - - +
147D GLY 5.8 0.2 + - - -
148D LEU* 4.6 0.6 - - - +
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Residues in contact with ASP 111 (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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74D ARG* 4.3 17.7 + - - +
107D LYS* 3.1 37.5 + - - +
108D GLU* 3.8 8.1 - - - +
109D LEU 3.2 0.4 - - - -
110D ARG* 1.3 83.0 - - - +
112D HIS* 1.3 75.8 + - + +
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Residues in contact with HIS 112 (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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74D ARG* 3.5 47.0 + - + +
77D THR* 3.8 23.3 - - + +
78D SER* 3.8 33.2 + - - +
81D TYR* 3.6 30.5 - - + +
82D ARG* 5.1 2.4 + - - -
108D GLU* 3.1 27.3 + - + +
111D ASP* 1.3 90.1 - - + +
113D ALA* 1.3 63.4 + - - +
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Residues in contact with ALA 113 (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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81D TYR* 4.1 17.7 - - + +
84D ALA 5.5 0.2 - - - +
109D LEU* 2.9 40.3 + - + +
110D ARG* 4.3 8.7 - - - +
112D HIS* 1.3 81.6 - - - +
114D ASP* 1.3 72.3 + - - +
115D SER* 3.7 1.0 + - - -
117D ILE* 4.1 14.4 - - + -
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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