Contacts of the helix formed by residues 107 - 122 (chain A) in PDB entry 2AY5
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 GLY 107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A THR* 3.0 26.4 + - - -
106A VAL* 1.3 74.8 - - - +
108A GLY* 1.3 68.6 + - - -
109A THR 3.2 1.1 - - - -
111A ALA 3.1 3.8 + - - -
257A SER* 5.1 0.2 - - - -
266A ARG* 3.1 15.0 + - - -
267A THR 3.6 20.6 - - - -
268A GLY* 3.9 6.1 - - - -
413A PLP 3.7 10.8 - - - -
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Residues in contact with GLY 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLY* 1.3 71.2 - - - -
109A THR* 1.3 54.8 + - - +
111A ALA* 3.0 5.9 + - - +
112A LEU* 2.8 36.6 + - - +
222A ASP* 6.0 0.4 - - - -
253A ALA* 4.4 2.6 - - - +
254A ALA 3.7 19.7 + - - -
255A SER* 3.9 10.4 + - - -
268A GLY* 4.2 0.8 - - - -
413A PLP 2.7 26.0 + - - -
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Residues in contact with THR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLY* 1.3 75.6 - - - +
110A GLY* 1.3 58.4 + - - +
112A LEU* 3.2 11.0 + - - +
113A ARG* 2.9 29.3 + - - +
140A TRP* 3.6 15.7 - - + -
142A ASN* 4.6 5.2 - - - +
146A ILE* 4.0 22.7 - - + -
413A PLP 2.8 29.3 + - - -
292B ARG 4.2 7.4 - - - +
294B THR 4.7 0.9 - - - -
295B TYR* 3.7 27.4 - - - +
296B SER* 3.6 13.4 + - - +
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Residues in contact with GLY 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A THR* 3.9 7.9 - - - -
106A VAL* 3.1 27.4 + - - -
107A GLY 3.1 0.6 + - - -
109A THR* 1.3 76.8 - - - +
111A ALA* 1.3 63.0 + - - +
113A ARG* 3.3 1.9 + - - +
114A GLN* 2.9 30.1 + - - +
295A TYR* 5.6 2.9 - - - -
294B THR 3.9 14.4 - - - -
295B TYR* 4.0 4.6 - - - +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A THR* 3.4 26.1 + - - +
107A GLY 3.1 6.8 + - - +
108A GLY* 3.0 12.9 + - - +
110A GLY* 1.3 75.7 - - - +
112A LEU* 1.3 56.0 - - - +
114A GLN* 3.3 1.6 + - - +
115A ALA* 2.8 30.7 + - - +
253A ALA* 3.7 15.3 - - + -
269A CYS 3.6 25.1 - - - +
270A LEU* 3.8 5.9 - - - +
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLY 2.8 20.8 + - - +
109A THR* 3.2 9.2 + - - +
111A ALA* 1.3 74.0 - - - +
113A ARG* 1.3 62.9 + - - +
115A ALA* 3.2 6.7 + - - +
116A LEU* 3.0 31.8 + - + +
140A TRP* 4.1 18.4 - - + -
143A HIS* 3.8 23.1 - - + +
146A ILE* 4.8 10.3 - - + -
187A LEU* 5.4 2.9 - - + -
220A LEU* 4.7 15.9 - - + -
222A ASP* 3.7 35.0 - - + +
253A ALA* 3.4 22.2 - - + -
413A PLP 4.2 5.8 - - + +
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Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A THR 2.9 11.0 + - - +
110A GLY 3.6 2.7 - - - +
112A LEU* 1.3 75.6 - - - +
114A GLN* 1.3 74.5 + - - +
116A LEU* 3.2 6.5 + - - +
117A GLU* 3.0 52.8 + - - +
146A ILE* 4.1 21.8 - - + +
149A PHE* 3.4 36.0 - - - -
150A MET* 4.3 8.1 - - - +
294A THR* 6.3 0.2 - - - +
113B ARG* 4.0 19.0 - - - +
117B GLU* 5.2 3.4 + - - -
293B GLN 3.0 28.6 + - - +
294B THR* 3.3 44.7 + - + +
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Residues in contact with GLN 114 (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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103A LEU* 4.3 7.9 - - + -
105A THR* 4.2 12.6 - - + -
110A GLY* 2.9 24.9 + - - +
111A ALA* 3.7 4.0 - - - +
113A ARG* 1.3 89.9 - - - +
115A ALA* 1.3 56.9 - - - +
117A GLU* 3.1 13.3 + - - +
118A LEU* 2.8 31.4 + - - +
270A LEU* 4.0 14.1 - - + -
290A LEU* 3.6 33.4 - - + +
291A ASN* 3.1 21.2 - - - +
294A THR* 4.2 13.5 + - - +
295A TYR* 3.8 11.4 + - - +
294B THR* 6.2 0.2 - - - +
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Residues in contact with ALA 115 (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 ALA 2.8 18.3 + - - +
112A LEU* 3.2 8.0 + - - +
114A GLN* 1.3 75.4 - - - +
116A LEU* 1.3 62.1 - - - +
118A LEU* 3.4 3.7 + - - +
119A ALA* 3.1 25.6 + - - +
185A MET* 5.1 1.1 - - - -
220A LEU* 3.7 33.2 - - + -
251A LEU* 4.2 9.5 - - + +
253A ALA* 5.4 0.9 - - + -
270A LEU* 3.7 22.1 - - + +
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Residues in contact with LEU 116 (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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112A LEU* 3.0 20.0 + - + +
113A ARG 3.5 7.9 - - - +
115A ALA* 1.3 76.6 - - - +
117A GLU* 1.3 61.4 + - - +
119A ALA* 3.7 4.5 + - - +
120A ARG* 3.1 25.3 + - - +
126A LEU* 4.4 4.1 - - + +
133A VAL* 5.4 1.6 - - + -
146A ILE* 3.8 18.4 - - + -
147A MET* 3.6 38.8 - - + -
150A MET* 3.6 27.2 - - + +
152A LEU* 3.8 12.6 - - + +
185A MET* 4.0 12.6 - - - -
187A LEU* 5.6 0.2 - - + -
220A LEU* 3.6 26.0 - - + -
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Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ARG* 3.0 56.8 + - - +
114A GLN* 3.1 16.1 + - - +
116A LEU* 1.3 74.6 - - - +
118A LEU* 1.3 63.9 + - - +
120A ARG* 3.5 9.0 + - - +
121A MET* 3.2 28.5 + - + +
150A MET* 3.5 19.4 - - + +
290A LEU* 3.7 21.3 - - + -
113B ARG* 5.1 3.6 + - - -
149B PHE* 4.9 13.7 - - - -
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Residues in contact with LEU 118 (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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114A GLN 2.8 18.7 + - - +
115A ALA 3.7 4.5 - - - +
117A GLU* 1.3 70.2 - - - +
119A ALA* 1.3 66.4 - - - +
121A MET* 3.0 19.1 + - - +
122A ALA* 3.1 12.8 + - - +
251A LEU* 4.8 9.4 - - + -
270A LEU* 4.4 11.7 - - + -
272A ALA* 4.7 9.6 - - + -
283A ALA* 4.5 2.7 - - + +
286A ALA* 3.7 31.9 - - + -
287A MET* 4.0 31.0 - - + -
290A LEU* 3.8 10.0 - - + +
6B LEU* 4.1 19.1 - - + -
9B LEU* 4.0 14.3 - - + +
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Residues in contact with ALA 119 (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 ALA 3.1 9.1 + - - +
116A LEU 4.0 0.9 - - - +
118A LEU* 1.3 78.7 - - - +
120A ARG* 1.3 58.8 + - - +
122A ALA* 3.2 5.6 + - - +
123A ASN* 2.9 27.0 + - - +
126A LEU* 3.7 14.4 - - + -
185A MET* 3.5 33.0 - - + -
251A LEU* 4.6 4.7 - - + +
5B MET* 3.9 21.3 - - - +
6B LEU* 5.0 3.6 - - - -
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Residues in contact with ARG 120 (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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116A LEU 3.1 18.6 + - - +
117A GLU* 3.8 9.8 + - - +
118A LEU 3.2 0.2 - - - -
119A ALA* 1.3 76.8 - - - +
121A MET* 1.3 61.5 + - + +
123A ASN 3.2 24.0 - - - +
124A PRO* 3.4 20.6 + - + +
126A LEU* 4.0 4.4 - - + +
150A MET* 2.7 48.8 + - - +
151A GLY* 4.1 12.9 + - - -
152A LEU* 3.7 26.4 - - + +
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Residues in contact with MET 121 (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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117A GLU* 3.2 15.3 + - - +
118A LEU* 3.0 13.3 + - - +
120A ARG* 1.3 79.3 - - - +
122A ALA* 1.3 61.1 + - - +
123A ASN* 3.5 0.3 + - - -
124A PRO* 4.5 6.4 - - - +
286A ALA* 5.0 14.1 - - + -
289A PHE* 4.2 16.6 - - + -
290A LEU* 4.0 23.8 - - + -
8B ASN 5.0 3.3 - - - +
9B LEU* 4.3 10.8 - - + -
10B LYS 6.1 0.2 - - - +
12B GLN* 3.8 27.8 - - + +
149B PHE* 4.6 10.8 - - + -
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Residues in contact with ALA 122 (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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118A LEU 3.1 8.5 + - - +
119A ALA 3.2 4.0 + - - +
121A MET* 1.3 79.2 - - - +
123A ASN* 1.3 61.6 + - - +
124A PRO* 4.3 2.6 - - - +
5B MET* 3.4 39.0 - - + +
6B LEU* 4.0 11.9 - - + -
8B ASN* 3.4 33.5 + - + +
9B LEU* 4.3 12.7 - - + +
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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
------------------------------------------------------------
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