Contacts of the helix formed by residues 110 - 133 (chain B) in PDB entry 2HYM
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 LEU 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B PRO* 1.3 70.8 - - - +
111B MET* 1.3 55.6 + - - +
112B LYS* 2.9 17.3 - - - -
113B GLU* 2.9 29.6 + - + +
114B ASP* 3.4 11.0 + - - +
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Residues in contact with MET 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLU* 5.4 1.9 - - - +
46B GLN* 4.5 24.0 - - + +
47B PHE* 3.9 27.7 - - + -
108B THR* 4.0 16.6 - - + -
109B PRO* 2.9 34.1 + - + +
110B LEU* 1.3 77.0 - - - +
112B LYS* 1.3 62.2 + - - +
113B GLU 3.2 0.2 - - - -
114B ASP* 3.2 24.1 + - + +
115B SER* 2.9 19.4 + - - -
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Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PHE* 5.3 3.6 - - - -
54B PRO* 5.4 14.1 - - + +
55B VAL* 4.7 4.1 - - - +
105B VAL 6.0 0.4 - - - +
106B THR* 3.9 31.1 - - + +
108B THR* 3.9 26.7 + - - +
109B PRO 3.0 20.2 + - - +
110B LEU* 2.9 13.4 - - - +
111B MET* 1.3 82.0 - - - +
113B GLU* 1.3 69.5 + - + +
115B SER* 3.1 14.5 + - - -
116B ILE* 3.5 20.9 - - + +
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Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 2.9 18.4 + - + +
112B LYS* 1.3 87.9 - - + +
114B ASP* 1.3 54.5 + - - +
115B SER 3.2 0.9 - - - -
116B ILE* 3.1 31.0 + - - +
117B LEU* 2.7 56.9 + - + +
120B ARG* 5.5 4.0 + - - -
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Residues in contact with ASP 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLU* 4.3 15.1 - - + +
110B LEU 3.4 4.6 + - - +
111B MET* 3.2 24.4 + - + +
113B GLU* 1.3 78.7 - - - +
115B SER* 1.3 56.2 + - - +
117B LEU* 3.3 17.6 + - - +
118B ALA* 3.0 28.2 + - - +
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Residues in contact with SER 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLU* 3.4 34.8 - - - +
47B PHE* 3.7 15.2 - - - -
55B VAL* 3.6 23.9 - - - +
111B MET 2.9 16.3 + - - -
112B LYS* 3.1 9.9 + - - -
114B ASP* 1.3 77.4 - - - +
116B ILE* 1.3 60.3 + - - +
118B ALA* 3.3 5.0 + - - +
119B VAL* 3.3 25.1 + - - +
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B PRO* 4.1 11.9 - - + +
55B VAL* 4.0 22.9 - - - -
58B GLU* 3.6 45.1 - - + +
62B GLN* 6.5 0.4 - - + -
112B LYS* 3.5 19.3 - - + +
113B GLU* 3.1 33.5 + - - +
115B SER* 1.3 76.0 - - - +
117B LEU* 1.3 53.5 + - + +
119B VAL* 3.1 6.8 + - + +
120B ARG* 2.8 38.7 + - + +
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B GLU* 2.7 45.2 + - + +
114B ASP* 3.5 19.1 - - - +
116B ILE* 1.3 74.3 - - + +
118B ALA* 1.3 62.0 + - - +
120B ARG* 3.4 29.7 - - - +
121B LYS* 3.0 26.2 + - - +
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B PRO* 3.8 24.7 - - + +
41B GLU* 4.5 3.1 - - - +
42B GLU* 4.2 17.3 - - + +
114B ASP 3.0 13.8 + - - +
115B SER 3.4 10.3 - - - +
117B LEU* 1.3 78.3 - - - +
119B VAL* 1.3 61.1 + - + +
121B LYS* 3.7 3.0 + - - +
122B TYR* 3.1 23.4 + - - +
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 4.6 10.1 - - + -
39B PRO* 4.3 5.6 - - + -
43B PHE* 3.7 31.9 - - + -
55B VAL* 4.1 4.9 - - + -
58B GLU 6.0 0.4 - - - -
59B MET* 3.8 28.0 - - + +
62B GLN* 5.0 3.1 - - + -
115B SER 3.3 14.6 - - - +
116B ILE* 3.1 7.3 + - + +
118B ALA* 1.3 74.3 - - + +
120B ARG* 1.3 66.4 + - - +
122B TYR* 3.2 5.8 + - + +
123B PHE* 2.9 55.8 + - + -
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Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLN* 3.8 26.0 + - + +
113B GLU* 5.5 4.4 + - - -
116B ILE* 2.8 23.7 + - + +
117B LEU* 3.3 30.0 + - - +
119B VAL* 1.3 77.3 - - - +
121B LYS* 1.3 58.7 + - - +
123B PHE* 3.3 2.9 + - - +
124B GLN* 3.0 27.4 + - + +
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Residues in contact with LYS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU 3.0 15.6 + - - +
118B ALA* 4.2 4.5 - - - +
120B ARG* 1.3 74.6 - - - +
122B TYR* 1.3 60.2 + - - +
124B GLN* 4.3 15.7 - - + -
125B ARG* 2.8 36.5 + - + +
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Residues in contact with TYR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PHE* 3.6 18.8 - + + -
37B GLY 3.8 18.2 - - - -
38B PHE* 3.7 13.0 + + - -
39B PRO* 3.6 18.2 - - + -
118B ALA 3.1 19.1 + - - +
119B VAL* 3.2 3.8 + - - +
121B LYS* 1.3 77.6 - - - +
123B PHE* 1.3 82.9 + + - +
125B ARG* 3.4 13.7 - - - +
126B ILE* 3.2 42.4 + - + +
146B GLU* 2.6 45.5 + - - +
147B ILE* 4.3 2.0 + - + -
150B SER* 3.2 24.3 + - - -
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Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B PHE* 5.5 0.2 - + - -
59B MET* 4.2 10.3 - - + -
62B GLN* 3.7 32.3 - - + +
63B ILE* 3.4 45.1 - - + -
66B LEU* 3.8 26.4 - - + +
67B PHE* 5.6 0.4 - + - -
119B VAL* 2.9 48.6 + - + +
122B TYR* 1.3 92.1 - + - +
124B GLN* 1.3 57.6 + - - +
126B ILE* 3.0 9.8 + - + +
127B THR* 2.8 31.5 + - - -
147B ILE* 3.7 22.7 - - + -
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Residues in contact with GLN 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLN* 5.0 1.3 - - - +
120B ARG* 3.0 17.4 + - + +
121B LYS* 3.2 19.3 + - + +
123B PHE* 1.3 76.3 - - - +
125B ARG* 1.3 61.3 + - - +
127B THR* 3.1 18.9 + - - +
128B LEU* 3.1 39.3 + - + +
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Residues in contact with ARG 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASP 3.5 22.4 + - - -
36B PHE* 3.3 48.1 + - + +
37B GLY 5.2 2.6 + - - -
121B LYS* 2.8 22.6 + - + +
122B TYR* 3.4 12.7 - - - +
124B GLN* 1.3 79.9 - - - +
126B ILE* 1.3 59.2 + - - +
128B LEU* 3.4 11.5 + - - +
129B TYR* 3.2 17.0 + - - +
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Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PHE* 3.6 29.2 - - + -
66B LEU* 4.7 5.6 - - + -
122B TYR* 3.2 47.6 - - + +
123B PHE* 3.0 16.0 + - + +
125B ARG* 1.3 76.4 - - - +
127B THR* 1.3 59.3 + - - +
129B TYR* 3.2 4.2 + - - +
130B LEU* 2.9 32.8 + - + +
143B VAL* 3.7 35.9 - - + -
146B GLU* 4.8 7.0 - - + -
147B ILE* 4.3 15.5 - - + -
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Residues in contact with THR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU* 3.8 21.4 - - + +
123B PHE 2.8 17.0 + - - -
124B GLN* 3.1 25.7 + - - +
126B ILE* 1.3 77.2 - - - +
128B LEU* 1.3 58.4 + - - +
130B LEU* 3.1 13.2 + - + +
131B LYS* 2.9 43.1 + - + +
135B TYR* 4.9 7.2 - - + +
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLN* 3.1 40.8 + - + +
125B ARG* 3.5 13.9 - - - +
126B ILE 3.2 0.2 - - - -
127B THR* 1.3 76.7 - - - +
129B TYR* 1.3 57.2 + - - +
131B LYS* 3.2 27.6 + - - +
132B GLU* 2.9 29.4 + - - +
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Residues in contact with TYR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ASP* 2.7 35.6 + - - +
34B HIS* 3.4 47.4 + - + +
36B PHE* 3.4 38.8 - + + -
125B ARG 3.2 3.3 + - - +
126B ILE 3.2 4.8 + - - +
128B LEU* 1.3 77.9 - - - +
130B LEU* 1.3 62.4 + - + +
132B GLU* 3.2 18.7 + - - +
133B LYS* 2.8 62.1 + - + +
139B ALA* 4.4 17.3 - - + -
142B VAL* 4.6 8.2 - - + +
143B VAL* 5.5 1.3 - - + -
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 4.8 13.7 - - + -
126B ILE* 2.9 29.4 + - + +
127B THR* 3.1 15.9 + - + +
129B TYR* 1.3 79.8 - - + +
131B LYS* 1.3 55.8 + - - +
133B LYS* 3.3 3.1 + - - -
134B LYS 2.9 7.4 + - - -
135B TYR* 2.7 54.2 + - + +
139B ALA* 4.6 10.8 - - + +
140B TRP* 3.8 47.3 - - + -
143B VAL* 3.8 22.0 - - + -
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Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B THR* 2.9 23.5 + - + +
128B LEU* 3.2 33.5 + - - +
130B LEU* 1.3 75.4 - - - +
132B GLU* 1.3 63.8 + - - +
134B LYS* 3.1 17.0 + - - +
135B TYR* 3.5 26.9 - - + +
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B HIS* 5.4 3.6 + - - -
128B LEU 2.9 16.2 + - - +
129B TYR* 3.5 26.7 - - - +
131B LYS* 1.3 77.5 - - - +
133B LYS* 1.3 69.4 + - + +
134B LYS* 3.5 5.9 + - - +
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LYS* 5.3 5.7 + - - +
32B ASP* 2.7 38.2 + - - +
34B HIS* 5.1 8.2 - - - -
129B TYR* 2.8 48.4 + - + +
130B LEU 4.1 2.0 - - - +
132B GLU* 1.3 92.9 - - + +
134B LYS* 1.3 63.4 + - - +
135B TYR 3.1 1.6 + - - +
136B SER* 2.6 31.4 + - - +
139B ALA* 3.7 21.5 - - + -
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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
------------------------------------------------------------
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