Contacts of the helix formed by residues 127 - 139 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A MET* 3.3 21.7 + - + +
109A ALA* 3.1 42.8 + - - +
110A MET* 4.0 10.2 - - - +
111A LYS* 3.2 23.0 + - + +
125A ILE 3.7 0.4 + - - -
126A SER* 1.3 72.5 - - - +
128A SER* 1.3 55.6 + - - +
130A SER* 3.8 8.3 - - - -
131A TYR* 2.7 55.1 + - + -
269B ALA* 5.7 2.3 - - - +
272B ARG* 2.9 30.4 + - - -
273B ALA* 5.8 3.6 - - - +
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Residues in contact with SER 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASP* 2.6 31.5 + - - -
106A MET* 3.0 36.2 + - - +
107A VAL* 4.0 4.3 - - - -
126A SER* 3.3 9.2 - - - -
127A GLU* 1.3 77.1 - - - +
129A THR* 1.3 64.7 + - - +
131A TYR* 3.5 2.4 + - - +
132A GLY* 3.1 17.5 + - - -
175A LYS* 5.6 4.9 + - - -
242A TRP* 5.3 1.0 - - - -
266B TYR* 4.6 2.3 + - - -
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Residues in contact with THR 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 3.6 13.3 - - - +
126A SER* 2.9 22.2 + - - +
128A SER* 1.3 74.5 - - - +
130A SER* 1.3 60.6 + - - +
132A GLY* 3.0 0.9 + - - +
133A LEU* 2.7 36.7 + - - +
178A ALA* 5.0 9.2 - - + -
179A LEU* 4.1 15.9 - - + +
182A THR* 5.0 7.2 - - - +
209A PRO* 6.4 0.7 - - + -
210A THR 4.6 2.5 - - - +
211A ALA* 3.4 41.7 + - + +
242A TRP* 5.9 3.8 - - + -
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Residues in contact with SER 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 3.6 24.8 - - - +
125A ILE* 3.8 23.1 - - - +
126A SER 2.9 18.6 + - - -
127A GLU* 3.1 11.0 + - - -
129A THR* 1.3 77.7 + - - +
131A TYR* 1.3 64.5 + - - +
133A LEU* 3.4 3.4 + - - +
134A LYS* 3.1 45.9 + - - +
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Residues in contact with TYR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A MET* 4.3 10.5 - - + -
111A LYS* 4.0 20.3 + - - -
127A GLU* 2.7 58.8 + - + +
128A SER 4.1 1.8 - - - +
130A SER* 1.3 73.7 - - - +
132A GLY* 1.3 64.2 + - - +
134A LYS* 3.4 9.7 + - + +
135A THR* 2.8 32.6 + - + +
265B LEU* 4.6 19.7 - - + -
266B TYR* 3.2 25.6 - + + -
269B ALA* 3.8 29.5 - - + +
272B ARG* 5.2 6.6 + - - -
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Residues in contact with GLY 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A SER 3.1 12.2 + - - -
129A THR 3.0 6.5 + - - -
131A TYR* 1.3 77.7 - - - +
133A LEU* 1.3 58.8 + - - +
135A THR* 2.6 21.6 + - - -
136A LEU* 3.2 12.8 + - - +
179A LEU* 3.8 20.2 - - - +
266B TYR* 3.2 13.3 + - - -
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TRP* 4.2 16.8 - - + -
115A TYR* 4.2 7.2 - - + -
125A ILE* 5.4 3.4 - - + -
129A THR 2.7 19.2 + - - +
130A SER* 3.8 4.3 - - - +
132A GLY* 1.3 70.4 - - - +
134A LYS* 1.3 71.6 + - - +
136A LEU* 3.0 7.8 + - + +
137A GLN* 2.9 59.5 + - + +
179A LEU* 3.8 9.0 - - + +
182A THR* 4.2 22.2 - - + -
183A LEU* 4.0 38.6 - - + +
186A TRP* 4.5 4.9 - - + -
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Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LYS* 5.9 0.6 - - - +
114A PRO* 4.4 17.0 - - - +
115A TYR* 3.6 16.9 + - - +
125A ILE* 5.3 1.8 - - - +
130A SER* 3.1 43.2 + - - +
131A TYR* 3.9 11.7 - - + +
133A LEU* 1.3 85.7 - - - +
135A THR* 1.3 62.5 + - + +
137A GLN* 3.0 32.2 + - - +
138A LYS* 3.0 46.2 + - - +
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Residues in contact with THR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A TYR* 4.7 23.0 - - + -
71A ALA* 4.7 9.0 - - - +
131A TYR* 2.8 22.7 - - + +
132A GLY* 2.6 22.3 + - - -
134A LYS* 1.3 77.0 - - + +
136A LEU* 1.3 61.6 + - - +
138A LYS* 3.4 10.9 + - - +
139A LEU* 3.1 33.1 + - - +
265B LEU* 5.6 7.0 - - + -
266B TYR* 3.2 32.2 + - + +
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA* 4.5 14.8 - - + -
72A MET 4.7 1.6 - - - +
73A MET* 3.3 37.8 - - + +
89A ILE* 3.6 43.7 - - + -
132A GLY 3.2 12.5 + - - +
133A LEU* 3.0 11.0 + - + +
135A THR* 1.3 85.2 + - - +
137A GLN* 1.3 59.8 + - - +
138A LYS 3.4 0.3 + - - -
139A LEU* 3.6 30.4 + - + +
152A ILE* 4.2 5.2 - - - +
179A LEU* 4.1 20.4 - - + +
183A LEU* 4.2 12.1 - - + -
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Residues in contact with GLN 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A TYR* 3.0 24.0 + - - -
133A LEU* 2.9 38.9 + - + +
134A LYS* 3.0 34.3 + - - +
136A LEU* 1.3 77.6 - - - +
138A LYS* 1.3 63.8 + - + +
139A LEU 3.5 0.4 - - - -
151A THR* 3.6 23.0 - - - +
152A ILE* 4.7 8.8 + - - +
153A LEU* 6.0 0.5 - - - +
183A LEU* 5.6 0.2 - - + -
186A TRP* 3.3 44.8 - - + +
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Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LYS* 3.0 39.4 + - - +
135A THR* 4.2 6.8 - - - +
137A GLN* 1.3 83.8 - - + +
139A LEU* 1.3 65.3 + - - +
140A LYS* 3.5 12.6 + - - +
151A THR* 4.3 5.9 - - - +
265B LEU* 2.9 34.7 - - - +
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TRP* 3.8 8.3 - - + -
59A ALA* 3.7 31.2 - - + +
60A VAL 3.8 29.8 - - - +
61A TYR* 3.9 19.3 - - + +
71A ALA* 5.4 0.4 - - + -
72A MET* 4.9 2.7 - - - +
73A MET* 4.3 11.4 - - + +
135A THR 3.1 21.2 + - - +
136A LEU* 3.6 37.9 + - + +
137A GLN 3.5 1.4 - - - -
138A LYS* 1.3 79.8 - - - +
140A LYS* 1.3 64.7 - - - +
150A LYS 3.8 0.7 - - - +
151A THR* 3.4 16.6 - - - -
152A ILE 4.3 0.7 + - - -
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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