Contacts of the helix formed by residues 136 - 151 (chain B) in PDB entry 3SSB
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LEU 3.3 2.8 + - - -
134B SER 3.1 3.9 - - - -
135B GLY* 1.3 75.9 - - - +
137B ILE* 1.3 65.2 - - - -
138B ASP* 3.2 12.8 - - - -
139B VAL* 3.1 7.8 + - - +
140B VAL* 3.0 25.8 + - - +
191B ASP* 4.2 10.5 - - - -
192B VAL* 3.2 15.9 - - - +
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Residues in contact with ILE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TYR* 3.4 63.7 - - + +
79B VAL* 4.1 7.4 - - + -
80B THR* 4.3 1.6 - - - +
135B GLY 3.9 3.0 + - - -
136B GLY* 1.3 70.6 - - - -
138B ASP* 1.3 60.8 + - - +
140B VAL* 3.3 1.3 + - + +
141B ALA* 2.9 27.9 + - - +
176B VAL* 3.9 26.7 - - + +
177B GLU* 3.7 35.0 - - + +
180B ALA* 4.7 9.6 - - + -
191B ASP* 5.0 8.1 + - - +
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Residues in contact with ASP 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLY* 3.8 8.1 - - - -
137B ILE* 1.3 75.1 - - - +
139B VAL* 1.3 71.3 + - - +
142B HIS* 2.8 32.7 + - - +
173B GLY* 3.6 28.5 - - - +
174B THR* 4.6 2.0 - - - +
177B GLU* 3.1 15.4 - - - +
187B GLU 3.1 5.0 - - - +
188B ILE* 3.4 9.6 - - + -
189B GLY* 2.9 31.1 + - - -
190B GLU* 3.3 3.0 - - - +
191B ASP* 5.5 1.2 + - - +
997B CA 2.4 26.2 - - - -
57J ILE* 5.3 0.4 - - - -
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ALA* 4.1 24.9 - - + -
122B TYR* 4.5 3.4 - - + -
133B LEU* 3.7 20.9 - - + +
136B GLY* 3.1 8.9 + - - +
138B ASP* 1.3 92.8 + - - +
140B VAL* 1.3 64.5 + - - +
142B HIS* 3.2 7.8 + - - +
143B GLU* 3.0 32.8 + - - +
189B GLY* 3.9 20.6 - - - +
192B VAL* 4.1 17.0 - - + -
202B LEU* 5.7 0.7 - - + -
57J ILE* 4.1 23.3 - - + -
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ALA* 4.6 6.5 - - - +
76B TYR* 3.8 40.4 - - + +
77B ALA* 3.8 9.2 - - + +
80B THR* 4.3 2.0 - - - +
120B MET* 3.8 6.6 - - + +
122B TYR* 3.4 35.2 - - + +
134B SER* 3.6 21.8 - - - +
136B GLY 3.0 16.7 + - - +
137B ILE 3.7 6.5 - - - +
139B VAL* 1.3 74.9 - - - +
141B ALA* 1.3 58.5 + - - +
143B GLU* 3.2 4.9 + - - +
144B LEU* 3.0 26.6 + - + +
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Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B THR* 3.5 26.1 - - + +
137B ILE 2.9 18.2 + - - +
140B VAL* 1.3 71.3 - - - +
142B HIS* 1.3 57.8 + - - +
144B LEU* 3.8 0.9 - - - +
145B THR* 2.6 39.6 + - - -
172B PHE 4.2 0.2 - - - +
173B GLY* 3.7 11.9 - - - +
176B VAL* 3.5 33.7 - - + -
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Residues in contact with HIS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ASP 2.8 19.8 + - - +
139B VAL 3.3 4.9 - - - +
141B ALA* 1.3 77.1 - - - +
143B GLU* 1.3 63.6 + - - +
145B THR 3.3 1.0 + - - -
146B HIS* 3.2 6.9 + - - -
166B GLU* 3.3 13.5 - - - -
169B SER* 2.8 55.4 + - - +
170B ASP* 2.8 30.9 + - - -
173B GLY* 3.9 1.0 - - - -
188B ILE* 5.1 1.3 - - + +
203B ARG* 3.6 6.7 - - - -
999B ZN 2.1 37.1 - - - -
56D ASN* 3.6 9.6 + - - -
57J ILE* 3.3 22.2 - - + +
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Residues in contact with GLU 143 (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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113B ALA* 3.5 18.2 - - + +
114B PHE* 3.4 28.2 - - - +
115B TRP* 3.6 11.9 + - - +
120B MET* 4.1 17.5 - - + -
122B TYR* 4.4 7.2 - - + +
139B VAL* 3.0 19.0 + - - +
140B VAL 3.2 5.8 + - - +
142B HIS* 1.3 78.6 - - - +
144B LEU* 1.3 63.9 + - - +
146B HIS* 3.0 22.2 + - - +
147B ALA 3.6 0.9 + - - -
55D ILE 3.5 3.1 - - - +
56D ASN* 2.4 30.7 - - - +
57J ILE* 3.0 27.7 + - - +
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ALA* 4.5 4.9 - - - +
80B THR* 3.3 38.6 - - + -
81B TYR* 4.5 3.1 - - - +
84B TYR* 5.3 3.1 - - + -
93B TYR* 4.0 32.3 - - + +
100B ILE* 4.2 24.9 - - + -
115B TRP* 4.9 3.1 - - + -
120B MET* 3.7 32.4 - - + -
140B VAL* 3.0 16.5 + - + +
143B GLU* 1.3 76.6 - - - +
145B THR* 1.3 61.7 + - - +
147B ALA* 3.0 25.5 + - + +
148B VAL* 3.2 10.6 + - + +
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Residues in contact with THR 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TYR* 2.9 32.0 + - - +
141B ALA* 2.6 26.8 + - - +
142B HIS 3.6 5.6 - - - -
143B GLU 3.2 0.2 - - - -
144B LEU* 1.3 76.4 - - - +
146B HIS* 1.3 57.1 + - - +
148B VAL* 3.1 8.5 + - + +
149B THR* 2.9 27.4 + - - +
168B ILE* 3.6 40.6 - - + +
169B SER* 3.7 9.9 - - - +
172B PHE* 3.6 11.9 - - + +
173B GLY 4.5 0.2 + - - -
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Residues in contact with HIS 146 (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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115B TRP* 4.0 17.4 - - + -
142B HIS* 3.2 12.5 + - - -
143B GLU* 3.0 16.1 + - - +
145B THR* 1.3 76.7 - - - +
147B ALA* 1.3 56.8 + - - +
149B THR* 3.6 4.2 + - - +
150B ASP* 2.9 28.8 + - - +
157B TYR* 4.0 0.4 - + - -
165B ASN* 2.7 36.2 + - - -
166B GLU* 3.2 9.0 - - - -
169B SER* 3.2 18.2 + - - -
999B ZN 2.1 35.8 - - - -
55D ILE* 3.4 26.8 - - + +
56D ASN* 3.4 12.7 + - - -
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Residues in contact with ALA 147 (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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93B TYR* 3.5 23.8 - - + -
115B TRP* 3.5 46.3 - - + +
143B GLU 3.6 2.4 + - - -
144B LEU* 3.0 14.2 + - + +
146B HIS* 1.3 73.7 - - - +
148B VAL* 1.3 66.3 - - - +
150B ASP* 3.2 4.0 + - - +
151B TYR* 3.0 27.7 + - - +
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Residues in contact with VAL 148 (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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84B TYR* 3.9 38.1 - - + +
90B ARG* 4.0 23.3 - - - +
93B TYR* 3.7 28.0 - - + -
144B LEU* 3.2 12.8 + - + +
145B THR* 3.1 9.1 + - - +
147B ALA* 1.3 78.9 - - - +
149B THR* 1.3 55.0 + - - +
151B TYR* 3.3 1.4 + - - +
152B THR* 2.6 36.0 + - + +
268B TYR* 4.9 2.9 - - + -
271B LEU* 3.9 21.8 - - + -
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Residues in contact with THR 149 (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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145B THR 2.9 17.9 + - - -
146B HIS 3.8 4.7 - - - -
148B VAL* 1.3 75.6 - - - +
150B ASP* 1.3 61.3 + - - +
152B THR* 3.1 13.2 + - - -
153B ALA 3.2 1.6 + - - -
154B GLY 2.8 25.3 + - - +
155B LEU* 3.9 33.0 - - + +
165B ASN* 3.8 31.9 + - - +
168B ILE* 3.4 25.8 - - - +
169B SER* 5.2 0.3 + - - -
271B LEU* 3.9 8.1 - - + +
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Residues in contact with ASP 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B TRP* 3.8 16.6 + - + +
117B GLY* 4.5 8.7 - - - +
146B HIS 2.9 19.2 + - - +
147B ALA* 3.3 9.2 - - - +
149B THR* 1.3 77.9 - - - +
151B TYR* 1.3 72.9 + - + +
152B THR 3.4 1.2 + - - +
154B GLY* 3.9 16.7 + - - -
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Residues in contact with TYR 151 (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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90B ARG* 4.2 3.6 + - - +
93B TYR* 3.6 46.4 + + - +
94B ASP* 3.6 28.7 - - + +
115B TRP* 4.8 6.3 - + - -
117B GLY 4.8 7.1 + - - -
147B ALA 3.0 21.6 + - - +
148B VAL 3.7 1.1 - - - +
149B THR 3.3 0.2 - - - -
150B ASP* 1.3 89.3 - - - +
152B THR* 1.3 62.7 + - - +
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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