Contacts of the helix formed by residues 117 - 135 (chain D) in PDB entry 4AY1
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 SER 117 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B THR* 6.1 2.7 - - - -
287B SER* 5.7 3.1 + - - -
115D VAL 3.2 0.8 + - - -
116D ASP* 1.3 80.6 - - - +
118D SER* 1.3 63.6 + - - +
119D THR* 3.5 14.0 + - - +
120D SER* 3.0 37.1 + - - -
121D ARG* 3.1 25.9 + - - +
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Residues in contact with SER 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ASN* 6.3 1.1 - - - -
117D SER* 1.3 70.9 - - - +
119D THR* 1.3 73.2 + - - +
121D ARG* 3.2 23.2 + - - +
122D LEU* 3.1 24.6 + - - +
161D GLU* 5.1 1.6 + - - -
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Residues in contact with THR 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B THR* 2.9 42.7 + - + +
289B PRO* 4.2 8.0 + - - +
290B GLY 4.8 0.7 - - - -
291B ALA* 4.4 24.2 - - + +
292B ALA 5.9 0.3 + - - -
299B SER* 5.4 4.2 + - - -
331B ASN* 5.3 2.9 - - - +
332B GLN* 3.8 10.3 - - - +
117D SER* 3.3 10.4 + - - +
118D SER* 1.3 82.5 - - - +
120D SER* 1.3 62.3 + - - +
122D LEU* 3.2 5.4 + - - +
123D GLU* 3.0 26.1 + - - +
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Residues in contact with SER 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D ASN* 3.8 28.0 - - - +
113D PRO 3.5 5.1 + - - -
114D MET* 2.6 30.2 + - - +
116D ASP* 5.1 0.2 - - - +
117D SER* 3.0 25.6 + - - -
119D THR* 1.3 84.6 + - - +
121D ARG* 1.3 55.1 + - - +
123D GLU* 3.5 8.3 + - - +
124D PHE* 3.1 26.7 + - - +
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Residues in contact with ARG 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D MET* 3.4 24.2 - - - +
115D VAL* 2.9 40.3 + - - +
116D ASP 4.3 1.0 - - - -
117D SER* 3.1 34.9 + - - +
118D SER* 3.2 20.4 + - - +
120D SER* 1.3 74.9 - - - +
122D LEU* 1.3 61.3 + - - +
124D PHE* 3.4 1.0 + - - +
125D ILE* 2.9 38.5 + - + +
154D HIS* 4.7 10.0 + - - -
157D VAL* 3.7 18.2 - - - +
158D LEU* 4.4 17.7 - - + +
161D GLU* 3.0 45.6 + - - +
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Residues in contact with LEU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ALA* 6.0 4.9 - - + -
292B ALA* 6.0 4.7 - - + +
118D SER 3.1 17.2 + - - +
119D THR* 3.6 5.6 - - - +
121D ARG* 1.3 77.2 - - + +
123D GLU* 1.3 65.7 + - - +
125D ILE* 3.3 14.2 + - + +
126D ASN* 2.9 66.3 + - - +
161D GLU* 5.8 4.3 - - + +
165D ALA* 6.5 0.2 - - + -
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Residues in contact with GLU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA* 3.9 12.2 + - - +
297B GLU 4.9 4.3 - - - +
298B SER* 5.2 1.4 - - - -
299B SER* 3.2 40.8 + - - +
68D ASN 4.6 2.8 - - - +
69D ASN* 3.9 20.4 - - + +
70D LYS* 3.8 25.5 + - + +
119D THR 3.0 16.4 + - - +
120D SER* 3.6 9.4 - - - +
122D LEU* 1.3 77.3 - - - +
124D PHE* 1.3 59.3 + - - +
126D ASN* 3.9 7.2 + - - +
127D SER* 3.2 22.7 + - - -
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Residues in contact with PHE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D ILE* 3.8 28.9 - - + -
69D ASN 3.1 20.8 + - - +
71D VAL* 4.1 7.9 - - + -
101D ILE* 3.6 18.8 - - + -
111D PHE* 5.8 2.7 - + - -
114D MET* 3.5 38.8 - - + -
120D SER 3.1 7.9 + - - +
121D ARG 3.6 2.7 - - - +
123D GLU* 1.3 74.6 - - - +
125D ILE* 1.3 70.4 + - + +
127D SER* 2.8 24.9 + - - -
128D ILE* 2.8 51.8 + - + +
140D LEU* 5.0 2.2 - - + -
142D VAL* 6.2 0.9 - - + -
158D LEU* 4.4 12.8 - - + -
162D LEU* 4.7 12.3 - - + -
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Residues in contact with ILE 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ARG 2.9 27.8 + - - +
122D LEU* 3.3 14.6 + - + +
124D PHE* 1.3 83.6 - - + +
126D ASN* 1.3 64.9 + - - +
128D ILE* 3.2 7.8 + - - +
129D ILE* 3.1 28.9 + - + +
158D LEU* 4.9 6.5 - - + +
161D GLU* 3.8 43.5 - - + +
162D LEU* 4.0 25.6 - - + +
165D ALA* 3.5 28.5 - - + -
166D PHE* 5.3 0.2 - - + -
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Residues in contact with ASN 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B ALA* 4.5 17.8 - - - +
293B GLY 5.6 1.2 + - - -
297B GLU* 4.8 24.3 + - + +
122D LEU* 2.9 46.4 + - - +
123D GLU* 3.9 6.1 - - - +
125D ILE* 1.3 75.4 - - - +
127D SER* 1.3 66.1 + - - +
129D ILE* 3.6 8.6 + - - +
130D LEU* 3.1 25.5 + - - +
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Residues in contact with SER 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D LYS* 3.4 31.7 - - - +
71D VAL* 2.9 28.0 + - - +
123D GLU 3.2 11.9 + - - -
124D PHE* 2.8 17.2 + - - -
126D ASN* 1.3 78.8 - - - +
128D ILE* 1.3 57.2 + - - +
130D LEU* 4.0 4.4 - - - +
131D PHE* 3.0 33.1 + - - +
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Residues in contact with ILE 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D VAL* 3.6 18.6 - - + -
99D LEU* 5.3 2.7 - - + -
101D ILE* 3.6 31.4 - - + -
124D PHE* 2.8 39.7 + - + +
125D ILE* 3.3 10.8 - - - +
127D SER* 1.3 74.9 + - - +
129D ILE* 1.3 67.8 + - - +
130D LEU 3.3 0.2 + - - -
131D PHE* 3.3 1.6 + - + +
132D LEU* 2.9 39.6 + - + +
140D LEU* 4.1 16.8 - - + -
162D LEU* 4.4 2.2 - - + -
166D PHE* 3.9 29.6 - - + -
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Residues in contact with ILE 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D ILE* 3.1 17.3 + - + +
126D ASN* 4.1 8.7 - - - +
128D ILE* 1.3 76.1 - - - +
130D LEU* 1.3 64.6 + - - +
132D LEU* 4.0 0.9 - - - +
133D ARG* 3.1 35.6 + - + +
165D ALA* 3.8 38.6 - - + +
166D PHE* 3.9 20.4 - - + -
169D ASP* 3.7 30.1 - - + +
178D LEU* 4.2 13.5 - - + -
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Residues in contact with LEU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B GLU* 4.4 22.7 - - + +
126D ASN 3.1 16.2 + - - +
127D SER* 4.0 5.8 - - - +
129D ILE* 1.3 80.9 - - - +
131D PHE* 1.3 55.8 + - + +
133D ARG* 3.8 3.2 - - - +
134D ASN* 2.5 72.4 + - + +
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Residues in contact with PHE 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D VAL* 3.8 28.5 - - + -
72D ILE* 4.9 1.1 - - - -
73D ILE* 3.4 26.5 - - + -
78D GLU* 5.1 1.8 - - - -
82D TYR* 3.3 24.0 - + - -
99D LEU* 3.7 29.2 - - + -
127D SER 3.0 21.1 + - - +
128D ILE 3.9 0.9 - - - +
130D LEU* 1.3 80.9 - - - +
132D LEU* 1.3 63.1 + - + +
134D ASN* 4.6 0.4 - - - -
135D HIS* 3.0 58.7 + + - +
137D PHE* 3.8 17.7 - + - -
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Residues in contact with LEU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LEU* 3.9 27.1 - - + -
128D ILE* 2.9 43.4 + - + +
129D ILE 4.0 2.2 - - - +
131D PHE* 1.3 80.2 - - + +
133D ARG* 1.3 61.9 + - - +
136D ASN* 3.1 4.5 + - - -
137D PHE* 2.9 55.6 + - + +
139D GLY* 3.7 35.7 - - - +
140D LEU* 4.0 6.1 - - + +
166D PHE* 4.2 3.6 - - + -
178D LEU* 4.0 24.7 - - + -
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Residues in contact with ARG 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ILE* 3.1 30.4 + - + +
130D LEU* 3.8 4.3 - - - +
132D LEU* 1.3 76.8 - - - +
134D ASN* 1.3 66.3 + - - +
135D HIS 3.2 0.9 + - - -
136D ASN* 3.3 11.2 + - - +
137D PHE 5.1 2.9 + - - -
138D ASP* 6.0 0.6 - - - +
169D ASP* 2.8 31.1 + - - +
170D PHE* 5.0 1.4 - - - +
173D SER* 3.9 14.6 + - - -
175D LYS* 4.0 45.1 + - - +
176D GLU 3.0 29.7 + - - +
177D ARG* 4.5 1.0 - - - +
178D LEU* 3.5 30.4 - - + +
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Residues in contact with ASN 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D LEU* 2.5 50.7 + - + +
131D PHE* 4.1 3.4 - - - +
133D ARG* 1.3 75.6 - - - +
135D HIS* 1.3 73.5 + - + +
136D ASN 3.8 0.5 + - - -
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Residues in contact with HIS 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D TYR* 3.5 48.0 + + + +
85D ILE* 4.0 12.0 - - - +
86D ASN* 4.7 1.1 - - - +
131D PHE* 3.0 61.3 + + - +
134D ASN* 1.3 88.5 + - + +
136D ASN* 1.3 71.7 + - - +
137D PHE* 3.3 25.2 + - + -
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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
------------------------------------------------------------
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