Contacts of the helix formed by residues 136 - 152 (chain A) in PDB entry 5FSJ
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 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU 3.2 7.6 + - - -
134A SER 3.1 3.0 - - - -
135A GLY* 1.3 77.4 - - - +
137A ILE* 1.3 66.5 + - - -
138A ASP* 3.2 13.0 - - - -
139A VAL* 3.0 10.2 + - - +
140A VAL* 3.0 23.4 + - - +
191A ASP* 4.4 10.5 - - - -
192A VAL* 3.4 10.3 - - - +
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TYR* 3.8 47.7 - - + +
79A VAL* 3.8 19.5 - - + -
80A THR* 5.2 0.4 - - - +
135A GLY 3.9 3.4 + - - -
136A GLY* 1.3 72.1 - - - +
138A ASP* 1.3 60.1 + - - +
140A VAL* 3.3 1.0 + - - +
141A ALA* 2.9 28.4 + - - +
173A GLY 4.9 0.4 - - - -
176A VAL* 4.0 16.2 - - + +
177A GLU* 3.8 29.8 - - + +
180A ALA* 3.5 31.4 - - + -
182A LYS 5.2 4.7 - - - +
191A ASP* 5.0 7.5 + - - +
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Residues in contact with ASP 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLY* 3.9 7.6 - - - -
137A ILE* 1.3 82.3 - - - +
139A VAL* 1.3 68.5 + - - +
142A HIS* 2.8 30.9 + - - +
173A GLY* 3.6 28.1 - - - +
174A THR* 4.5 1.8 - - - +
177A GLU* 3.1 16.8 - - + +
187A GLU 3.2 4.5 - - - +
188A ILE* 3.4 10.9 - - + +
189A GLY* 2.9 31.2 + - - -
190A GLU* 3.3 3.6 - - - +
191A ASP* 5.5 1.4 + - - +
1009A CA 2.4 25.7 - - - -
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Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ALA* 4.3 24.2 - - + -
122A TYR* 4.5 3.1 - - + -
130A PHE* 6.2 0.7 - - + -
133A LEU* 3.6 27.1 - - + +
136A GLY* 3.0 9.1 + - - +
138A ASP* 1.3 90.3 + - - +
140A VAL* 1.3 65.3 + - - +
142A HIS* 3.2 6.7 + - - +
143A GLU* 3.0 34.4 + - - +
188A ILE* 5.5 1.1 - - + -
189A GLY* 4.1 19.1 - - - -
192A VAL* 4.2 12.6 - - + -
1001A VAL* 4.3 21.3 - - + -
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Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP 4.6 2.0 - - - +
73A ALA* 4.6 4.0 - - - +
76A TYR* 3.8 41.3 - - + +
77A ALA* 3.8 9.0 - - - +
80A THR* 4.3 2.2 - - - +
120A MET* 3.9 6.1 - - + +
122A TYR* 3.4 35.2 - - + +
134A SER* 3.7 22.2 - - - +
136A GLY 3.0 13.1 + - - +
137A ILE 3.3 5.8 + - - +
139A VAL* 1.3 73.9 - - - +
141A ALA* 1.3 59.7 + - - +
143A GLU* 3.2 4.0 + - - +
144A LEU* 3.0 27.1 + - + +
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Residues in contact with ALA 141 (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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80A THR* 3.5 26.2 - - + +
137A ILE 2.9 16.8 + - - +
140A VAL* 1.3 74.1 - - - +
142A HIS* 1.3 58.3 + - - +
144A LEU* 3.9 0.7 - - - +
145A THR* 2.7 38.9 + - - +
172A PHE 4.3 0.2 - - - +
173A GLY* 3.7 13.2 - - - +
176A VAL* 3.6 29.4 - - + -
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Residues in contact with HIS 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASP 2.8 20.0 + - - +
139A VAL* 3.4 8.1 - - - +
141A ALA* 1.3 76.6 - - - +
143A GLU* 1.3 80.3 + - - +
145A THR 3.3 1.7 + - - -
146A HIS* 3.2 6.5 + - - -
166A GLU* 3.0 17.0 - - - -
169A SER* 2.8 54.1 + - - +
170A ASP* 2.8 28.2 + - - -
173A GLY* 3.9 1.2 - - - -
188A ILE* 5.1 3.2 - - + +
203A ARG* 3.4 10.6 + - - -
1001A VAL* 4.3 7.2 - - + +
1006A ZN 3.6 1.8 - - - -
1007A ZN 2.0 37.3 - - - -
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Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ALA* 3.2 14.5 - - + +
114A PHE* 3.5 31.9 - - - +
115A TRP* 3.7 8.3 + - - +
120A MET* 4.0 18.4 - - + -
122A TYR* 4.5 7.2 - - + +
139A VAL* 3.0 20.9 + - - +
140A VAL 3.8 3.1 - - - +
142A HIS* 1.3 89.2 - - - +
144A LEU* 1.3 62.9 + - - +
146A HIS* 3.0 31.8 + - - +
147A ALA 3.7 2.3 + - - -
1001A VAL* 2.7 39.9 + - - +
1006A ZN 4.2 1.6 - - - -
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Residues in contact with LEU 144 (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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77A ALA* 4.5 6.3 - - - +
80A THR* 3.6 35.0 - - + -
81A TYR 4.7 0.4 - - - +
84A TYR* 5.6 0.4 - - - -
93A TYR* 3.9 29.6 - - + -
100A ILE* 4.1 17.9 - - + -
115A TRP* 4.7 3.8 - - + -
120A MET* 3.7 29.8 - - + -
140A VAL* 3.0 16.0 + - + +
143A GLU* 1.3 76.4 - - - +
145A THR* 1.3 58.3 + - - +
147A ALA* 2.9 31.2 + - + +
148A VAL* 3.2 7.5 + - + +
1008A OXY 3.6 20.9 - - - +
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Residues in contact with THR 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 2.7 32.5 + - - +
141A ALA* 2.7 22.8 + - - +
142A HIS* 3.6 6.1 - - - -
143A GLU 3.2 0.4 - - - -
144A LEU* 1.3 74.9 - - - +
146A HIS* 1.3 64.8 + - - +
148A VAL* 3.1 8.8 + - + +
149A THR* 2.9 22.7 + - - +
168A ILE* 3.8 32.5 - - + +
169A SER* 3.7 15.5 - - - +
172A PHE* 3.6 10.4 - - + +
176A VAL* 5.8 0.2 - - - +
271A LEU* 5.4 0.2 - - + -
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Residues in contact with HIS 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TRP* 3.9 20.0 - - + -
142A HIS* 3.2 9.4 + - - -
143A GLU* 3.0 27.1 + - - +
145A THR* 1.3 76.4 - - - +
147A ALA* 1.3 56.1 + - - +
149A THR* 3.4 4.0 + - - -
150A ASP* 2.9 38.7 + - - +
157A TYR* 4.0 10.2 + + - -
165A ASN* 2.8 31.9 + - - -
166A GLU* 3.1 10.8 - - - -
169A SER* 3.4 18.8 + - - -
1006A ZN 3.7 2.1 - - - -
1007A ZN 2.1 37.1 - - - -
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Residues in contact with ALA 147 (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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93A TYR* 3.6 20.0 - - + -
115A TRP* 3.4 49.4 - - + +
143A GLU 3.7 2.2 + - - -
144A LEU* 2.9 13.9 + - + +
146A HIS* 1.3 76.9 - - - +
148A VAL* 1.3 64.5 + - - +
150A ASP* 3.2 3.3 + - - +
151A TYR* 3.2 28.8 + - - -
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Residues in contact with VAL 148 (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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84A TYR* 4.0 34.5 - - + +
90A ARG* 3.9 25.8 - - - +
93A TYR* 3.8 25.8 - - + -
144A LEU 3.2 11.4 + - - +
145A THR* 3.1 9.5 + - + +
147A ALA* 1.3 76.9 - - - +
149A THR* 1.3 61.7 + - - +
151A TYR* 3.2 2.8 + - - +
152A THR* 2.8 29.9 + - + +
268A TYR* 4.9 3.1 - - + -
271A LEU* 4.0 20.4 - - + -
1008A OXY 4.4 4.3 - - - +
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Residues in contact with THR 149 (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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145A THR 2.9 16.9 + - - -
146A HIS* 3.6 7.6 - - - -
148A VAL* 1.3 76.4 - - - +
150A ASP* 1.3 61.9 + - - +
152A THR* 3.0 13.1 + - - -
153A ALA 3.4 0.3 + - - -
154A GLY 2.8 26.8 + - - +
155A LEU* 4.0 28.5 - - + +
165A ASN* 3.6 32.5 + - - +
168A ILE* 3.6 24.1 - - - +
169A SER* 5.2 0.3 + - - -
271A LEU* 3.8 8.2 - - + +
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Residues in contact with ASP 150 (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 TRP* 3.4 28.4 + - + +
117A GLY* 4.9 3.5 - - - -
146A HIS* 2.9 21.9 + - - +
147A ALA* 3.2 6.5 + - - +
149A THR* 1.3 77.1 - - - +
151A TYR* 1.3 64.8 + - + +
152A THR 3.6 0.9 + - - +
154A GLY* 4.2 13.6 - - - -
155A LEU 5.1 1.9 - - - +
165A ASN* 4.2 15.9 + - - -
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Residues in contact with TYR 151 (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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90A ARG* 4.3 3.9 + - - +
93A TYR* 3.5 46.9 + + - +
94A ASP* 3.6 30.3 + - + +
115A TRP* 5.4 5.2 - + - -
117A GLY 5.8 2.5 - - - -
147A ALA 3.2 21.3 + - - +
148A VAL 3.2 1.8 + - - +
149A THR 3.1 0.4 - - - -
150A ASP* 1.3 81.6 - - + +
152A THR* 1.3 62.9 + - - +
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Residues in contact with THR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 3.4 37.5 - - - +
148A VAL* 2.8 22.7 + - + +
149A THR* 3.0 8.9 + - - -
150A ASP 3.3 0.7 - - - +
151A TYR* 1.3 81.2 - - - +
153A ALA* 1.3 73.4 + - - +
154A GLY* 3.2 1.8 + - - -
271A LEU* 3.6 22.1 - - - +
272A THR* 4.0 17.0 - - + -
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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