Contacts of the helix formed by residues 127 - 139 (chain B) in PDB entry 2ORY
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 GLU 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A ALA* 4.1 11.8 - - + +
272A ARG* 4.3 9.0 + - - -
106B MET* 3.2 20.8 + - - +
109B ALA* 3.0 40.0 + - + +
110B MET* 4.1 6.3 - - - +
111B LYS* 2.9 41.1 - - - +
125B ILE 3.6 0.8 + - - -
126B SER* 1.3 72.1 - - - +
128B SER* 1.3 58.4 + - - +
130B SER* 4.0 3.4 + - - -
131B TYR* 2.8 63.6 + - + +
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Residues in contact with SER 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A TYR* 4.4 11.7 + - - -
104B ASP* 2.6 31.4 + - - -
106B MET* 3.1 28.0 + - - +
107B VAL* 4.2 2.9 - - - -
126B SER* 3.6 9.2 - - - -
127B GLU* 1.3 78.4 - - - +
129B THR* 1.3 63.9 + - - +
131B TYR* 4.2 1.6 - - - +
132B GLY* 3.1 18.4 + - - -
175B LYS* 5.5 6.4 - - - +
179B LEU* 5.4 0.2 - - - +
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Residues in contact with THR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ILE* 3.6 10.0 - - - +
126B SER* 2.9 27.7 + - - +
128B SER* 1.3 75.7 - - - +
130B SER* 1.3 60.2 + - - +
132B GLY* 3.6 0.4 - - - +
133B LEU* 2.8 32.4 + - - +
175B LYS* 6.2 3.1 - - + -
178B ALA* 4.3 16.8 - - + -
179B LEU* 4.1 15.9 - - + +
182B THR* 5.0 6.2 - - - +
209B PRO* 6.4 0.4 - - + -
210B THR 4.8 2.0 - - - +
211B ALA* 3.1 38.3 + - + +
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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
----------------------------------------------------------
111B LYS* 3.8 22.2 + - - +
125B ILE* 3.6 23.8 - - - +
126B SER 2.9 17.6 + - - -
127B GLU* 3.6 14.1 + - - -
129B THR* 1.3 78.7 + - - +
131B TYR* 1.3 65.7 + - - +
133B LEU* 3.2 4.7 + - - +
134B LYS* 3.1 38.5 + - - +
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Residues in contact with TYR 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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265A LEU* 3.6 45.3 + - + +
266A TYR* 3.7 39.7 - + + -
269A ALA* 3.8 15.4 - - + +
272A ARG* 4.7 5.4 + - - -
69B ASN* 5.5 0.9 - - - +
106B MET* 5.6 0.4 - - - -
111B LYS* 4.2 15.3 + - - -
127B GLU* 2.8 63.5 + - + +
128B SER 4.2 0.2 - - - +
130B SER* 1.3 75.3 - - - +
132B GLY* 1.3 62.5 + - - +
134B LYS* 3.3 17.6 + - + +
135B THR* 3.0 28.8 + - + +
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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
----------------------------------------------------------
128B SER 3.1 16.0 + - - -
129B THR 3.2 3.1 + - - -
131B TYR* 1.3 77.6 - - - +
133B LEU* 1.3 61.2 + - - +
135B THR* 2.4 26.2 + - - -
136B LEU* 3.2 12.1 + - - +
179B LEU* 3.9 19.4 - - - +
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TRP* 4.1 28.3 - - + -
115B TYR* 4.2 10.3 - - + +
125B ILE* 5.2 3.6 - - + -
129B THR 2.8 20.1 + - - +
130B SER* 3.6 5.2 - - - +
132B GLY* 1.3 71.9 - - - +
134B LYS* 1.3 60.0 + - + +
136B LEU* 3.0 9.5 + - + +
137B GLN* 2.9 61.5 + - + +
179B LEU* 3.9 5.2 - - + +
182B THR* 4.1 12.1 - - + -
183B LEU* 3.9 39.5 - - + +
186B TRP* 4.4 4.5 - - + -
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Residues in contact with LYS 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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111B LYS* 3.3 29.9 - - - +
114B PRO* 6.1 4.7 - - - -
115B TYR* 5.8 2.9 - - - +
130B SER* 3.1 30.7 + - - +
131B TYR* 3.6 21.3 - - + +
132B GLY 3.3 0.2 - - - -
133B LEU* 1.3 76.9 - - + +
135B THR* 1.3 62.8 + - + +
137B GLN* 3.3 18.0 + - - +
138B LYS* 3.1 49.4 + - - +
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Residues in contact with THR 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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61B TYR* 3.7 54.0 - - + +
69B ASN* 5.2 6.6 + - + +
71B ALA* 4.8 7.4 - - - +
131B TYR* 3.0 17.9 + - + +
132B GLY* 2.4 31.7 + - - -
134B LYS* 1.3 76.3 - - + +
136B LEU* 1.3 60.5 + - - +
138B LYS* 3.3 5.3 + - - +
139B LEU* 3.0 33.0 + - - +
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Residues in contact with LEU 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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71B ALA* 4.3 17.9 - - + -
72B MET 5.0 0.9 - - - -
73B MET* 3.4 36.9 - - + +
89B ILE* 4.0 39.0 - - + -
132B GLY 3.4 13.7 - - - +
133B LEU* 3.0 12.4 + - - +
135B THR* 1.3 83.3 + - - +
137B GLN* 1.3 61.5 + - - +
138B LYS 3.4 0.5 + - - -
139B LEU* 3.6 28.5 + - + +
152B ILE* 4.1 4.8 - - - +
179B LEU* 4.0 20.0 - - + +
183B LEU* 4.0 20.0 - - + -
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Residues in contact with GLN 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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115B TYR* 2.9 30.0 + - - -
133B LEU* 2.9 30.8 + - + +
134B LYS* 3.3 27.8 + - - +
136B LEU* 1.3 77.3 - - - +
138B LYS* 1.3 63.2 + - + +
139B LEU 3.6 0.4 - - - -
151B THR* 3.8 21.0 - - - +
152B ILE* 4.4 11.3 - - - +
153B LEU* 6.1 0.3 - - - +
186B TRP* 3.2 51.7 - - + +
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Residues in contact with LYS 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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134B LYS* 3.1 44.3 + - - +
135B THR* 4.0 4.5 - - - +
137B GLN* 1.3 84.5 + - + +
139B LEU* 1.3 66.1 + - - +
140B LYS* 3.5 17.4 + - - +
151B THR* 4.3 5.1 - - - +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TRP* 3.5 15.3 - - + -
59B ALA* 3.6 32.5 - - + +
60B VAL 3.7 25.6 - - - +
61B TYR* 4.1 21.8 - - + +
71B ALA 5.0 0.4 - - - +
72B MET* 5.0 1.8 - - - -
73B MET* 4.5 9.4 - - + +
135B THR 3.0 16.8 + - - +
136B LEU* 3.8 34.5 - - + +
137B GLN 3.6 1.0 - - - -
138B LYS* 1.3 80.8 - - - +
140B LYS* 1.3 67.1 + - - +
151B THR* 3.4 15.6 - - - -
152B ILE 4.1 1.2 + - - -
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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