Contacts of the helix formed by residues 122 - 138 (chain B) in PDB entry 2HXO
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 THR 122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A TYR* 6.0 0.2 - - - -
64B GLY 5.1 1.7 + - - -
68B ASP* 2.7 30.4 + - - +
114B GLN* 4.0 2.2 + - - -
120B TRP 4.1 7.6 - - - +
121B GLY* 1.3 75.5 - - - -
123B VAL* 1.3 65.7 + - - +
124B ALA 3.5 0.9 - - - -
125B PRO* 3.4 10.5 - - - +
126B ARG* 3.3 39.8 + - - +
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Residues in contact with VAL 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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64B GLY 4.2 2.9 - - - +
67B THR* 4.0 10.1 - - + -
68B ASP* 3.8 35.0 - - + +
71B VAL* 3.9 35.2 - - + -
111B LEU* 4.0 9.0 - - + -
114B GLN* 4.0 24.4 + - + +
121B GLY 3.6 0.6 - - - -
122B THR* 1.3 75.8 - - - +
124B ALA* 1.3 66.1 + - - +
126B ARG* 3.2 5.5 + - + +
127B ILE* 3.0 40.4 + - + +
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A TRP* 4.2 12.8 - - + +
114B GLN* 4.7 9.2 - - + +
115B LEU* 3.3 34.1 - - + +
118B THR 5.9 1.1 - - - +
121B GLY* 4.6 3.3 + - - +
123B VAL* 1.3 77.9 - - - +
125B PRO* 1.3 66.1 - - + +
127B ILE* 3.1 10.5 + - - +
128B PHE* 2.8 29.6 + - - +
153B MSE 4.3 4.9 - - - +
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Residues in contact with PRO 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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190A TRP* 3.9 24.7 - - + +
193A LEU* 3.7 33.7 - - + -
198A TYR* 4.3 7.2 - - + +
201A THR* 3.6 7.8 + - + +
121B GLY 3.2 22.9 - - - +
122B THR* 3.4 15.5 - - - +
124B ALA* 1.3 95.9 - - + +
126B ARG* 1.3 55.1 + - - +
128B PHE* 3.6 7.4 - - + +
129B GLU* 2.8 30.0 + - - +
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Residues in contact with ARG 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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198A TYR* 3.3 30.1 + - + +
68B ASP* 2.6 44.1 + - - -
71B VAL* 6.4 1.6 - - + -
72B THR* 4.8 8.7 + - - -
122B THR* 3.3 31.9 + - - +
123B VAL* 3.2 5.1 + - + +
124B ALA 3.2 0.8 - - - -
125B PRO* 1.3 75.2 - - - +
127B ILE* 1.3 59.5 + - + +
129B GLU* 3.6 7.2 - - - +
130B SER* 2.7 34.6 + - - -
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 4.3 13.9 - - + -
75B VAL* 6.0 1.8 - - + -
93B VAL* 5.0 3.6 - - + -
97B LEU* 4.1 38.1 - - + -
111B LEU* 4.6 9.9 - - + -
115B LEU* 6.2 2.2 - - + -
123B VAL* 3.0 31.4 + - + +
124B ALA* 3.5 9.0 - - - +
126B ARG* 1.3 75.5 - - + +
128B PHE* 1.3 63.9 + - - +
130B SER* 3.2 8.5 + - - -
131B LEU* 3.0 34.0 + - + +
153B MSE 3.2 29.4 - - + -
157B LEU* 5.9 4.3 - - + -
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Residues in contact with PHE 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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190A TRP* 3.6 30.3 - + + -
200A PHE* 3.5 30.8 - + - -
201A THR* 4.4 6.5 - - + +
204A VAL* 4.8 5.8 - - + -
124B ALA 2.8 17.1 + - - +
125B PRO* 3.6 9.0 - - + +
127B ILE* 1.3 78.4 - - - +
129B GLU* 1.3 55.8 + - - +
131B LEU* 4.1 0.8 - - - +
132B GLY* 2.9 28.1 + - - -
146B PHE* 3.3 39.5 - + - -
149B SER* 3.5 28.3 - - - -
150B SER* 3.7 20.0 - - - -
153B MSE 3.3 23.1 - - + -
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Residues in contact with GLU 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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197A ALA 4.6 2.0 - - - +
198A TYR* 3.1 39.2 - - + -
199A PRO* 3.8 0.2 - - - +
200A PHE* 3.1 14.6 + - - +
201A THR* 2.4 48.0 + - - +
125B PRO 2.8 15.3 + - - +
126B ARG* 3.6 7.0 - - - +
127B ILE 3.2 0.2 - - - -
128B PHE* 1.3 72.7 - - - +
130B SER* 1.3 64.7 + - - +
132B GLY* 3.9 0.2 - - - -
133B ARG* 2.9 68.7 + - - +
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Residues in contact with SER 130 (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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75B VAL* 4.8 8.9 - - - +
93B VAL* 4.1 28.7 - - - +
126B ARG 2.7 19.8 + - - -
127B ILE* 3.4 10.1 - - - -
129B GLU* 1.3 80.5 - - - +
131B LEU* 1.3 63.4 + - - +
133B ARG* 4.0 3.8 + - - +
134B GLN* 3.5 26.0 + - - +
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Residues in contact with LEU 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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90B VAL* 4.2 27.1 - - + +
93B VAL* 3.7 30.5 - - + -
94B ALA* 5.5 0.7 - - + +
127B ILE* 3.0 18.4 + - + +
128B PHE 4.1 2.0 - - - +
130B SER* 1.3 74.2 - - - +
132B GLY* 1.3 66.1 + - - +
134B GLN* 3.1 10.5 + - - +
135B VAL* 3.1 21.3 + - - +
149B SER* 4.1 22.2 - - - +
152B LEU* 4.2 15.0 - - + -
153B MSE 3.7 39.3 - - + +
156B ILE* 5.2 8.1 - - + -
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Residues in contact with GLY 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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200A PHE* 3.4 30.7 - - - -
128B PHE 2.9 11.8 + - - -
131B LEU* 1.3 77.1 - - - +
133B ARG* 1.3 62.7 + - - +
135B VAL* 2.9 4.7 + - - +
136B GLN* 2.9 23.6 + - - +
149B SER* 3.4 18.9 + - - -
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Residues in contact with ARG 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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196A ASP 4.8 1.2 + - - -
197A ALA* 2.7 31.3 + - - +
199A PRO* 3.5 17.5 - - + +
200A PHE* 4.1 4.8 - - + -
129B GLU* 2.9 39.1 + - - +
130B SER* 4.3 3.1 - - - +
131B LEU 3.4 0.2 - - - -
132B GLY* 1.3 76.2 - - - +
134B GLN* 1.3 71.3 + - - +
136B GLN* 3.0 36.5 + - - +
137B ALA* 3.0 15.9 + - - +
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Residues in contact with GLN 134 (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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86B PRO* 3.3 36.2 - - + +
89B ALA* 3.6 23.0 - - + +
90B VAL* 3.6 22.7 - - + +
93B VAL* 5.9 1.1 - - + -
130B SER 3.5 18.5 + - - +
131B LEU 3.1 7.3 + - - +
132B GLY 3.1 0.6 - - - -
133B ARG* 1.3 86.6 - - - +
135B VAL* 1.3 62.0 + - - +
137B ALA* 3.1 6.5 + - - +
138B MSE 2.9 34.9 + - - +
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Residues in contact with VAL 135 (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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131B LEU 3.1 12.4 + - - +
132B GLY* 2.9 8.9 + - - +
134B GLN* 1.3 78.6 - - + +
136B GLN* 1.3 61.5 + - - +
138B MSE 3.1 24.3 + - - +
140B VAL* 3.4 33.3 + - + +
145B TRP* 3.9 19.7 - - + +
148B ALA* 3.9 24.5 - - + -
149B SER* 3.8 15.0 - - - +
152B LEU* 4.2 20.4 - - + -
228B ILE* 4.6 5.8 - - + -
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Residues in contact with GLN 136 (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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199A PRO* 5.6 5.5 - - - +
200A PHE* 3.7 25.0 - - - +
203A ALA* 5.8 0.3 - - - +
132B GLY 2.9 13.9 + - - +
133B ARG* 3.0 39.1 + - - +
135B VAL* 1.3 76.9 - - - +
137B ALA* 1.3 57.1 + - - +
139B GLY* 3.0 19.9 + - - -
140B VAL 4.2 0.8 + - - +
145B TRP* 4.0 42.6 - - + +
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Residues in contact with ALA 137 (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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86B PRO* 3.8 23.0 - - + +
133B ARG 3.0 19.1 + - - +
134B GLN* 3.1 11.2 + - - +
136B GLN* 1.3 77.7 - - + +
138B MSE 1.3 59.3 + - - +
139B GLY 3.2 1.2 + - - -
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Residues in contact with MSE 138 (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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86B PRO* 3.6 19.5 - - + -
87B GLN* 3.6 22.4 - - + +
90B VAL* 5.2 2.5 - - - -
134B GLN 2.9 21.7 + - - +
135B VAL* 3.3 18.4 - - - +
136B GLN 3.0 0.8 - - - -
137B ALA* 1.3 77.5 - - - +
139B GLY* 1.3 60.8 + - - +
140B VAL* 3.4 7.2 - - + +
225B LEU* 3.6 36.8 - - + +
228B ILE* 3.8 20.9 - - + -
229B THR* 2.9 36.7 - - + +
232B HIS* 4.0 13.2 + - - +
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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