Contacts of the helix formed by residues 114 - 126 (chain D) in PDB entry 3VON
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 SER 114 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D ARG* 5.0 3.8 - - - -
18D GLU* 3.3 25.4 - - - -
73D TYR* 3.5 3.8 - - - -
109D TRP* 4.3 4.0 - - - -
112D SER 4.8 3.1 - - - -
113D TYR* 1.3 75.7 - - - +
115D ILE* 1.3 65.6 + - - +
116D LYS* 3.4 20.4 - - - +
117D VAL* 3.1 28.5 + - - +
118D VAL* 3.3 13.3 + - - +
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Residues in contact with ILE 115 (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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15D LEU* 4.7 3.8 - - + -
18D GLU* 3.3 20.9 + - + +
33D TRP* 3.7 30.1 - - + -
46D TRP* 3.7 48.9 - - + +
47D THR 6.2 0.2 - - - -
48D GLY* 5.8 0.7 - - - -
67D VAL* 4.8 21.3 - - + -
69D CYS* 4.7 6.5 - - - -
73D TYR* 3.4 14.0 + - + +
78D PRO* 5.4 3.1 - - + -
114D SER* 1.3 73.3 - - - +
116D LYS* 1.3 63.6 + - - +
118D VAL* 3.0 21.0 + - + +
119D LEU* 3.0 23.2 + - + +
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Residues in contact with LYS 116 (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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18D GLU* 4.3 1.2 + - - -
21D GLU* 3.1 27.2 + - - +
26D VAL* 3.8 16.1 - - + +
31D VAL* 5.7 1.1 - - + -
33D TRP* 3.7 39.9 - - + -
114D SER* 3.4 15.0 + - - +
115D ILE* 1.3 78.1 - - - +
117D VAL* 1.3 59.9 + - - +
119D LEU* 3.4 3.4 + - - +
120D GLN* 2.9 60.0 + - + +
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Residues in contact with VAL 117 (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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105D VAL* 4.0 20.4 - - + -
112D SER 5.4 0.9 - - - +
113D TYR* 4.0 31.0 - - + -
114D SER* 3.1 34.2 + - - +
116D LYS* 1.3 79.4 - - + +
118D VAL* 1.3 57.6 + - - +
120D GLN* 3.8 13.3 - - - +
121D GLU* 3.0 32.2 + - + +
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Residues in contact with VAL 118 (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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78D PRO* 4.6 9.9 - - + -
80D VAL* 4.0 26.2 - - + -
103D ILE* 5.7 4.3 - - + +
105D VAL* 4.1 12.1 - - + -
106D LEU* 4.7 14.8 - - + -
109D TRP* 3.7 27.4 - - + -
114D SER 3.6 13.2 - - - +
115D ILE* 3.0 13.1 + - + +
117D VAL* 1.3 76.7 - - - +
119D LEU* 1.3 65.2 + - + +
121D GLU* 3.3 4.1 + - - +
122D LEU* 3.1 35.2 + - + +
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Residues in contact with LEU 119 (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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31D VAL* 3.6 22.0 - - + +
32D SER 3.3 35.0 - - - +
33D TRP* 3.8 20.6 - - + -
48D GLY* 4.0 16.4 - - - -
49D MET 4.0 6.3 - - - +
50D ILE* 3.9 23.5 - - + +
65D LEU* 4.4 9.0 - - + -
67D VAL* 5.3 5.8 - - + -
80D VAL* 5.7 0.9 - - + -
115D ILE* 3.0 22.2 + - + +
116D LYS 4.0 2.9 - - - +
118D VAL* 1.3 76.7 - - + +
120D GLN* 1.3 64.6 + - - +
122D LEU* 3.3 14.0 + - + +
123D ARG* 3.2 18.4 + - - +
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Residues in contact with GLN 120 (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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26D VAL* 5.5 2.6 - - - +
31D VAL* 3.7 28.5 - - + +
116D LYS* 2.9 53.5 + - + +
117D VAL* 3.8 12.3 - - - +
119D LEU* 1.3 75.0 - - - +
121D GLU* 1.3 61.3 + - - +
123D ARG* 3.5 5.6 + - - +
124D ARG* 3.2 29.3 + - + +
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Residues in contact with GLU 121 (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 ILE* 4.4 7.0 - - + -
104D PRO* 3.8 25.5 - - - +
105D VAL* 3.9 30.8 - - + +
117D VAL* 3.0 19.5 + - + +
118D VAL* 3.7 5.4 - - - +
120D GLN* 1.3 76.2 - - - +
122D LEU* 1.3 58.8 + - - +
124D ARG* 2.8 46.4 + - - +
125D LEU* 2.9 41.5 + - + +
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Residues in contact with LEU 122 (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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50D ILE* 3.8 23.8 - - + -
65D LEU* 3.9 17.9 - - + -
80D VAL* 4.6 6.1 - - + -
82D PHE* 4.2 17.7 - - + -
88D MET* 3.5 15.3 - - + +
91D ILE* 5.2 1.6 - - + -
98D VAL* 4.5 11.0 - - + -
103D ILE* 4.5 26.7 - - + -
118D VAL* 3.1 31.4 + - + +
119D LEU* 3.3 12.1 + - + +
121D GLU* 1.3 77.4 - - - +
123D ARG* 1.3 56.2 + - - +
125D LEU* 3.2 5.9 + - + -
126D MET* 3.0 34.8 + - + +
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Residues in contact with ARG 123 (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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28D ASP* 5.1 3.0 + - - -
30D THR* 3.4 48.8 + - - +
31D VAL* 4.2 6.3 - - + -
50D ILE* 3.6 11.2 - - + -
51D ILE* 3.2 25.9 + - - +
52D GLY 4.2 3.2 + - - -
53D PRO* 3.4 32.8 - - + +
54D PRO* 3.6 26.1 - - - +
119D LEU 3.2 7.2 + - - +
120D GLN* 3.6 10.1 - - - +
122D LEU* 1.3 79.0 - - - +
124D ARG* 1.3 60.9 + - + +
126D MET* 3.5 13.6 - - - +
127D MET* 3.4 23.7 - - + +
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Residues in contact with ARG 124 (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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120D GLN* 3.2 17.2 + - + +
121D GLU* 2.8 43.4 + - - +
122D LEU 3.2 0.2 - - - -
123D ARG* 1.3 73.2 - - + +
125D LEU* 1.3 59.7 + - - +
126D MET 3.0 4.7 - - - -
127D MET* 2.8 49.3 + - + +
128D SER* 3.5 3.1 + - - -
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Residues in contact with LEU 125 (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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88D MET* 3.6 12.3 - - + -
102D SER 5.3 3.6 - - - +
103D ILE* 3.9 24.0 - - + -
104D PRO* 3.8 34.1 - - + -
121D GLU* 2.9 35.4 + - + +
122D LEU* 3.2 8.0 + - - +
124D ARG* 1.3 79.4 - - + +
126D MET* 1.3 56.7 + - - +
127D MET 3.2 0.2 - - - -
128D SER* 3.2 21.6 - - - +
130D GLU* 5.7 3.6 - - - +
131D ASN* 3.0 29.8 + - - +
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Residues in contact with MET 126 (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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50D ILE* 3.8 28.7 - - + -
52D GLY* 4.8 0.2 - - - -
53D PRO* 3.8 20.9 - - + -
56D THR* 3.8 2.4 - - - +
58D TYR* 3.4 54.0 - - + -
63D TYR* 4.4 9.2 - - + -
82D PHE* 4.6 8.1 - - + -
86D ILE* 4.4 6.7 - - + -
88D MET* 3.7 23.8 - - - -
122D LEU* 3.0 31.1 + - + +
123D ARG* 3.5 18.8 - - - +
124D ARG 3.0 0.6 - - - -
125D LEU* 1.3 77.8 - - - +
127D MET* 1.3 57.2 + - - +
128D SER 3.2 3.9 + - - -
131D ASN* 4.6 0.7 - - - -
132D MET* 3.7 10.7 + - - +
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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