Contacts of the helix formed by residues 108 - 124 (chain D) in PDB entry 2HVY
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 ALA 108 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D ALA* 4.0 25.4 - - + +
26D ILE* 3.8 29.3 - - + +
27D ALA* 4.9 0.2 - - + -
105D PRO* 3.2 16.3 + - - +
107D LYS* 1.3 76.6 - - - +
109D ARG* 1.3 57.2 - - - +
110D ASP 3.4 2.2 - - - -
111D LEU* 3.2 12.4 + - + +
112D VAL* 2.9 31.4 + - + +
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Residues in contact with ARG 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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105D PRO* 3.7 19.8 - - + +
106D GLY 3.4 20.7 + - - +
107D LYS* 3.1 7.0 + - - +
108D ALA* 1.3 78.1 - - - +
110D ASP* 1.3 77.6 + - - +
112D VAL* 3.5 3.5 + - - +
113D GLU* 3.2 39.3 + - + +
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Residues in contact with ASP 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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107D LYS 4.6 4.3 + - - +
108D ALA 3.4 0.2 - - - -
109D ARG* 1.3 93.0 + - - +
111D LEU* 1.3 60.1 + - - +
113D GLU* 3.4 23.0 + - - +
114D GLU* 3.0 27.6 + - - +
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Residues in contact with LEU 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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19D LYS* 3.5 45.8 - - + +
22D GLN* 3.8 19.5 - - + +
23D ALA* 3.6 21.5 - - + +
26D ILE* 4.2 13.9 - - + -
107D LYS 5.4 0.2 + - - -
108D ALA* 3.2 15.8 + - + +
110D ASP* 1.3 76.3 - - - +
112D VAL* 1.3 58.8 + - - +
114D GLU* 3.4 23.7 + - - +
115D ILE* 3.1 33.7 + - - +
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Residues in contact with VAL 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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23D ALA* 4.4 7.2 - - + +
50D LYS* 4.5 17.9 - - + +
51D LEU* 4.0 25.7 - - + +
102D ILE* 4.1 24.0 - - + -
105D PRO* 3.9 21.5 - - + -
108D ALA* 2.9 21.0 + - + +
109D ARG 3.8 5.6 - - - +
111D LEU* 1.3 73.4 - - - +
113D GLU* 1.3 59.6 + - - +
115D ILE* 3.3 7.5 + - - +
116D ALA* 2.9 33.2 + - + +
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Residues in contact with GLU 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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109D ARG* 3.2 36.1 + - + +
110D ASP* 3.4 24.0 - - - +
111D LEU 3.3 0.2 - - - -
112D VAL* 1.3 78.2 - - + +
114D GLU* 1.3 61.4 + - - +
116D ALA* 4.0 4.8 - - - +
117D MET* 3.1 42.4 + - + +
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Residues in contact with GLU 114 (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* 5.8 0.2 - - + -
19D LYS* 3.6 34.4 + - + +
110D ASP 3.0 16.5 + - - +
111D LEU* 3.6 19.9 - - - +
112D VAL 3.3 0.2 - - - -
113D GLU* 1.3 75.9 - - - +
115D ILE* 1.3 60.9 + - + +
117D MET* 3.7 6.4 + - - +
118D LYS* 3.2 57.4 + - + +
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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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16D LEU* 4.5 14.4 - - + +
19D LYS* 3.6 37.5 - - + +
20D ALA* 3.7 14.8 - - - +
23D ALA* 3.9 12.8 - - + -
51D LEU* 3.9 32.8 - - + -
79D ILE* 4.2 13.0 - - + -
111D LEU* 3.1 21.0 + - + +
112D VAL 3.7 4.0 - - - +
114D GLU* 1.3 75.5 - - + +
116D ALA* 1.3 61.1 + - - +
118D LYS* 3.1 1.4 + - - +
119D VAL* 2.8 47.3 + - + +
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Residues in contact with ALA 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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50D LYS 5.5 0.2 - - - +
51D LEU* 5.3 1.6 - - + -
77D PRO* 4.0 25.1 - - + +
112D VAL* 2.9 24.7 + - + +
113D GLU* 4.0 6.1 - - - +
115D ILE* 1.3 74.9 - - - +
117D MET* 1.3 60.8 + - + +
119D VAL* 3.5 20.4 - - - +
120D LYS* 3.5 14.4 + - - +
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Residues in contact with MET 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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113D GLU* 3.1 31.9 + - + +
114D GLU* 4.0 7.0 - - - +
115D ILE 3.2 0.2 - - - -
116D ALA* 1.3 79.0 - - + +
118D LYS* 1.3 65.0 + - + +
120D LYS* 3.6 12.2 + - - +
121D GLU* 3.6 19.9 - - - +
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Residues in contact with LYS 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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16D LEU* 3.8 29.1 - - + +
19D LYS* 4.9 6.9 - - - +
114D GLU* 3.2 46.8 + - + +
115D ILE 3.1 3.6 + - - +
117D MET* 1.3 77.6 - - + +
119D VAL* 1.3 64.1 + - - +
121D GLU* 3.5 9.0 + - - +
122D LEU* 3.4 25.0 + - - +
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Residues in contact with VAL 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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10D PHE* 4.5 8.4 - - + -
16D LEU* 4.2 5.6 - - + -
77D PRO* 4.1 15.5 - - + -
78D TYR 3.8 22.2 - - - +
79D ILE* 3.6 31.6 - - + -
115D ILE* 2.8 31.6 + - + +
116D ALA* 3.5 16.6 - - - +
118D LYS* 1.3 75.4 - - - +
120D LYS* 1.3 63.1 + - - +
121D GLU 3.2 0.7 - - - -
122D LEU* 3.2 8.4 + - - +
123D MET* 2.9 35.4 + - + +
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Residues in contact with LYS 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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116D ALA 3.5 15.7 + - - +
117D MET* 3.7 9.4 - - - +
118D LYS 3.3 0.4 - - - -
119D VAL* 1.3 82.3 - - + +
121D GLU* 1.3 65.9 + - - +
123D MET* 3.7 10.3 + - + +
124D LYS* 3.2 39.4 + - + +
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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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117D MET 3.6 16.2 - - - +
118D LYS* 3.5 9.6 + - - +
119D VAL 3.2 0.6 - - - -
120D LYS* 1.3 83.8 - - - +
122D LEU* 1.3 64.1 + - + +
123D MET 3.3 0.2 - - - -
124D LYS* 3.5 47.2 + - - +
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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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10D PHE* 3.8 39.7 - - + +
11D GLU* 3.4 26.7 - - + +
12D VAL* 4.7 1.6 - - + -
13D PRO* 4.0 14.4 - - + -
16D LEU* 3.8 28.3 - - + -
118D LYS 3.4 11.6 + - - +
119D VAL* 3.2 9.1 + - - +
121D GLU* 1.3 75.9 - - + +
123D MET* 1.3 64.1 + - - +
124D LYS* 3.2 4.0 + - - -
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Residues in contact with MET 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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9D LYS* 5.5 1.1 - - - -
10D PHE* 3.7 23.8 - - + -
72D GLU* 3.7 33.0 - - + +
78D TYR* 3.3 28.9 - - + +
119D VAL* 2.9 23.6 + - + +
120D LYS* 3.8 12.6 - - + +
121D GLU 3.3 0.2 - - - -
122D LEU* 1.3 76.6 - - - +
124D LYS* 1.3 57.5 + - + +
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Residues in contact with LYS 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 LYS* 3.2 29.8 - - + +
121D GLU* 3.5 48.4 + - - +
122D LEU 3.2 4.0 - - - -
123D MET* 1.3 81.2 - - + +
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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