Contacts of the helix formed by residues 107 - 122 (chain B) in PDB entry 2AY6
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B THR* 2.8 29.2 + - - -
106B VAL* 1.3 77.4 - - - +
108B GLY* 1.3 62.3 + - - -
109B THR 3.3 0.4 - - - -
111B ALA* 3.2 3.1 + - - +
266B ARG* 3.4 13.8 - - - -
267B THR 3.5 23.3 - - - +
268B GLY* 4.0 5.6 - - - -
413B PLP 3.9 9.4 - - - -
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Residues in contact with GLY 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLY* 1.3 69.9 - - - -
109B THR* 1.3 65.4 + - - +
111B ALA* 3.2 5.4 + - - +
112B LEU* 3.0 27.3 + - - +
253B ALA* 4.5 2.8 - - - +
254B ALA 3.7 20.4 + - - -
255B SER* 3.8 12.2 - - - +
413B PLP 2.9 26.0 + - - -
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Residues in contact with THR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ARG 4.1 5.4 - - - +
294A THR 4.3 1.6 - - - +
295A TYR* 3.9 26.2 - - - +
296A SER* 3.9 6.1 - - - +
108B GLY* 1.3 77.1 - - - +
110B GLY* 1.3 62.2 + - - +
112B LEU* 3.0 21.1 + - - +
113B ARG* 3.1 12.6 + - - +
140B TRP* 3.3 21.6 - - + -
142B ASN* 3.8 20.9 - - - +
146B ILE* 4.3 12.0 - - + +
413B PLP 2.7 23.2 + - - -
414B 3IB 4.0 5.7 + - - -
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Residues in contact with GLY 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A THR 3.5 15.7 - - - -
295A TYR* 3.9 6.1 - - - +
105B THR* 4.0 6.1 - - - -
106B VAL* 3.1 27.2 + - - -
109B THR* 1.3 78.6 - - - +
111B ALA* 1.3 56.2 + - - +
113B ARG* 3.3 3.3 + - - +
114B GLN* 2.9 33.3 + - - +
295B TYR* 5.9 2.0 - - - -
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B THR* 3.3 25.5 + - + +
107B GLY 3.2 7.0 + - - +
108B GLY* 3.2 12.3 + - - +
109B THR 3.2 0.2 - - - -
110B GLY* 1.3 74.6 - - - +
112B LEU* 1.3 59.2 + - - +
114B GLN* 3.7 2.1 - - - +
115B ALA* 2.9 29.5 + - - +
253B ALA* 3.9 13.7 - - + -
269B CYS 3.6 25.8 - - - +
270B LEU* 4.1 6.5 - - + +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLY 3.0 17.6 + - - +
109B THR* 3.0 11.7 + - - +
111B ALA* 1.3 75.0 - - - +
113B ARG* 1.3 59.8 + - - +
115B ALA* 3.2 5.2 + - - +
116B LEU* 3.0 38.3 + - + +
140B TRP* 3.8 20.9 - - + -
143B HIS* 3.6 24.0 - - + +
146B ILE* 4.5 11.2 - - + -
187B LEU* 4.9 1.3 - - + -
220B LEU* 4.5 18.3 - - + +
222B ASP* 3.4 32.5 - - + +
253B ALA* 3.7 19.3 - - + -
413B PLP 4.3 2.9 - - + -
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Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ARG* 4.2 19.0 - - - +
117A GLU* 5.4 2.6 + - - -
293A GLN 2.7 36.3 + - - +
294A THR* 3.4 47.9 + - + +
109B THR 3.1 4.8 + - - +
110B GLY 3.6 3.6 - - - +
112B LEU* 1.3 74.7 - - - +
114B GLN* 1.3 68.9 + - - +
116B LEU* 3.1 3.4 + - - +
117B GLU* 2.9 59.7 + - + +
146B ILE* 3.9 22.8 - - + +
149B PHE* 3.4 28.7 - - - -
150B MET* 3.9 11.5 - - - +
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Residues in contact with GLN 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A THR* 6.1 0.2 - - - +
103B LEU* 3.6 22.9 - - + -
105B THR* 4.2 6.1 - - + -
110B GLY 2.9 18.5 + - - +
111B ALA* 3.7 9.2 - - - +
113B ARG* 1.3 85.2 - - - +
115B ALA* 1.3 57.9 + - - +
117B GLU* 4.4 5.1 - - - +
118B LEU* 3.1 29.1 + - - +
270B LEU* 4.1 9.2 - - + +
287B MET* 6.3 0.2 - - + -
290B LEU* 3.5 41.1 + - + +
291B ASN* 2.8 26.2 + - - +
294B THR* 4.3 8.8 + - - +
295B TYR* 3.7 13.4 + - - -
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ALA 2.9 19.6 + - - +
112B LEU* 3.3 8.3 - - - +
113B ARG 3.1 0.2 - - - -
114B GLN* 1.3 76.4 - - - +
116B LEU* 1.3 61.8 + - - +
118B LEU* 3.8 3.3 - - - +
119B ALA* 3.1 29.6 + - - +
185B MET* 4.2 1.1 - - - +
220B LEU* 3.7 25.1 - - + -
251B LEU* 4.0 7.8 - - + +
253B ALA* 5.1 0.2 - - + -
270B LEU* 3.6 27.3 - - + +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 3.0 22.6 + - + +
113B ARG 3.1 1.8 + - - +
115B ALA* 1.3 74.3 - - - +
117B GLU* 1.3 61.1 + - - +
119B ALA* 3.5 2.5 + - - +
120B ARG* 2.9 30.7 + - - +
126B LEU* 5.0 1.8 - - + +
133B VAL* 4.3 16.4 - - + -
146B ILE* 3.9 28.7 - - + -
147B MET* 3.9 30.7 - - + -
150B MET* 3.6 22.0 - - + +
152B LEU* 4.3 8.2 - - + +
185B MET* 3.9 25.4 - - - -
220B LEU* 4.2 10.3 - - + -
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Residues in contact with GLU 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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113A ARG* 5.4 2.2 + - - -
149A PHE* 4.7 15.7 - - + -
113B ARG* 2.9 55.0 + - + +
114B GLN* 3.8 10.1 - - - +
116B LEU* 1.3 74.3 - - - +
118B LEU* 1.3 60.1 + - - +
120B ARG* 3.0 25.7 + - - +
121B MET* 2.9 35.1 + - - +
150B MET* 3.4 16.3 - - + +
290B LEU* 3.8 21.3 - - + -
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Residues in contact with LEU 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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6A LEU* 4.5 19.1 - - + -
9A LEU* 3.9 24.9 - - + +
114B GLN 3.1 18.4 + - - +
115B ALA 3.8 3.6 - - - +
117B GLU* 1.3 75.3 - - - +
119B ALA* 1.3 64.5 + - - +
121B MET* 3.2 9.6 + - - +
122B ALA* 3.0 22.4 + - - +
251B LEU* 4.8 8.5 - - + -
270B LEU* 4.4 12.3 - - + -
272B ALA* 4.6 11.9 - - + -
283B ALA* 4.4 3.4 - - + +
286B ALA* 3.9 20.6 - - + -
287B MET* 3.9 32.1 - - + -
290B LEU* 3.7 9.3 - - + +
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Residues in contact with ALA 119 (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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5A MET* 3.4 25.6 - - + +
6A LEU* 5.0 2.5 - - - -
115B ALA 3.1 15.8 + - - +
116B LEU* 3.8 5.2 - - - +
118B LEU* 1.3 80.5 - - - +
120B ARG* 1.3 56.3 + - - +
122B ALA* 3.2 2.0 + - - -
123B ASN 3.0 24.3 + - - +
126B LEU* 4.5 11.2 - - + +
185B MET* 3.3 29.8 - - + -
251B LEU* 4.6 2.6 - - + +
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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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116B LEU 2.9 18.9 + - - +
117B GLU* 3.0 34.9 + - - +
119B ALA* 1.3 73.3 - - - +
121B MET* 1.3 69.1 + - - +
123B ASN 3.0 29.5 + - - +
124B PRO* 3.3 16.7 - - + +
126B LEU* 4.7 3.8 - - + +
150B MET* 3.3 41.4 + - - +
152B LEU* 3.8 25.8 - - + +
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Residues in contact with MET 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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8A ASN 5.0 4.0 - - - +
9A LEU* 4.9 9.4 - - + -
12A GLN* 4.3 15.5 - - - +
149A PHE* 4.2 15.0 - - + -
117B GLU* 2.9 21.3 + - + +
118B LEU* 3.2 9.8 + - + +
120B ARG* 1.3 78.1 - - - +
122B ALA* 1.3 62.1 + - - +
123B ASN* 4.3 0.3 - - - -
124B PRO* 4.4 6.8 - - - +
286B ALA* 4.6 19.5 - - - +
289B PHE* 3.8 30.7 - - + -
290B LEU* 4.0 19.7 - - + -
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Residues in contact with ALA 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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5A MET* 3.7 25.8 - - + +
6A LEU* 4.1 5.2 - - + -
8A ASN* 3.2 29.6 + - - +
9A LEU* 3.2 31.2 - - + +
118B LEU 3.0 7.2 + - - +
119B ALA 3.5 9.2 - - - +
120B ARG 3.1 0.2 - - - -
121B MET* 1.3 80.6 - - - +
123B ASN* 1.3 59.4 + - - +
124B PRO* 4.3 1.8 - - - +
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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
------------------------------------------------------------
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