Contacts of the helix formed by residues 134 - 152 (chain B) in PDB entry 6CM9
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 ASP 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PRO* 3.2 28.8 - - + +
103B ARG* 4.3 9.8 - - - +
132B ASP* 3.8 3.6 + - - +
133B GLU* 1.3 80.1 - - + +
135B PRO* 1.3 69.1 - - - +
136B TYR* 2.8 16.0 + - - +
137B VAL* 3.1 21.9 + - + +
138B ARG* 3.7 1.4 + - - +
148M ARG* 2.5 33.9 + - - +
149M PRO 5.5 1.2 - - - +
154M THR* 4.1 10.7 - - - +
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Residues in contact with PRO 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLU 3.3 5.8 - - - +
134B ASP* 1.3 87.2 - - - +
136B TYR* 1.3 61.8 + - - +
137B VAL 3.5 0.2 - - - -
138B ARG* 3.4 31.2 - - + +
139B LYS* 3.5 23.7 + - - +
173B ASN* 3.3 31.6 - - + +
176B VAL* 3.8 18.0 - - + +
154M THR* 4.5 13.4 - - + -
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Residues in contact with TYR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PRO* 4.2 9.2 - - + -
101B LEU* 3.8 12.9 - - + +
104B ALA* 3.6 30.3 - - + -
108B ARG* 2.8 16.8 + - - -
134B ASP* 2.8 11.0 + - - +
135B PRO* 1.3 77.8 - - - +
137B VAL* 1.3 62.2 + - - +
139B LYS* 3.3 36.6 - - - +
140B THR* 3.1 26.6 + - - -
116M GLU* 2.7 39.2 + - - -
134M TYR* 4.1 2.9 - + - -
149M PRO* 3.7 33.9 - - + -
153M VAL* 3.9 19.5 - - + -
154M THR* 4.4 11.5 - - + +
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PRO* 4.5 6.7 + - + +
103B ARG* 3.9 19.1 - - + +
104B ALA* 3.7 36.8 - - + +
107B VAL* 4.2 12.6 - - + -
129B CYS* 4.4 9.9 - - + +
132B ASP* 3.3 36.3 - - + +
134B ASP* 3.1 18.0 + - + +
136B TYR* 1.3 79.1 - - - +
138B ARG* 1.3 59.2 + - + +
140B THR* 3.4 1.3 + - - -
141B ALA* 2.9 26.5 + - - +
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Residues in contact with ARG 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B CYS 3.8 17.3 - - - +
130B LEU* 3.7 17.2 - - - +
131B LYS* 4.7 1.3 - - - +
132B ASP 3.3 28.1 + - - +
133B GLU 3.9 8.6 + - - -
134B ASP 3.7 3.6 + - - +
135B PRO* 3.4 34.6 - - + +
136B TYR 3.3 0.6 - - - -
137B VAL* 1.3 77.5 - - + +
139B LYS* 1.3 60.4 + - - +
141B ALA* 4.0 2.1 - - - +
142B ALA* 2.9 31.7 + - - +
168B LEU* 4.2 21.0 - - + +
171B ASP* 2.4 32.3 + - - +
173B ASN* 5.0 4.9 - - - +
176B VAL* 4.4 20.3 - - + +
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Residues in contact with LYS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PRO 3.5 15.1 + - - +
136B TYR* 3.3 40.3 + - - +
138B ARG* 1.3 77.8 - - - +
140B THR* 1.3 60.7 + - - +
142B ALA* 4.3 1.8 - - - -
143B VAL* 3.8 6.9 + - - +
175B MET* 4.1 26.9 - - + -
176B VAL* 4.2 17.4 - - - +
179B ASN* 3.4 41.9 - - - +
124M GLN* 3.2 45.1 + - + +
125M THR* 3.8 13.9 + - - -
153M VAL* 4.3 7.0 - - - +
154M THR* 6.2 0.9 - - - -
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Residues in contact with THR 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ALA* 3.4 37.1 - - - +
107B VAL* 3.9 5.2 - - + -
108B ARG* 3.7 40.8 + - + +
136B TYR* 3.1 16.3 + - - -
137B VAL 3.6 7.4 - - - -
138B ARG 3.1 0.2 - - - -
139B LYS* 1.3 79.2 + - - +
141B ALA* 1.3 59.7 + - - +
142B ALA 3.2 0.2 - - - -
143B VAL* 3.2 8.0 + - - +
144B CYS* 3.0 22.5 + - - +
119M ASP* 4.4 9.0 + - - +
124M GLN* 4.8 2.5 + - - -
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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
----------------------------------------------------------
107B VAL* 3.7 20.0 - - + -
126B LEU* 4.2 9.6 - - + +
129B CYS* 4.1 19.7 - - + +
130B LEU* 3.6 17.4 - - + +
137B VAL 2.9 18.5 + - - +
138B ARG 3.2 2.2 + - - +
140B THR* 1.3 73.5 - - - +
142B ALA* 1.3 65.2 + - - +
144B CYS* 3.2 3.4 + - - +
145B VAL* 3.0 27.0 + - - +
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 4.0 4.2 - - - +
138B ARG 2.9 16.8 + - - +
139B LYS* 4.4 1.1 - - - +
140B THR 3.2 0.2 - - - -
141B ALA* 1.3 78.3 - - - +
143B VAL* 1.3 60.9 + - - +
145B VAL* 3.4 13.2 + - - +
165B LEU* 4.0 10.3 - - + +
168B LEU* 4.1 13.7 - - + -
176B VAL* 4.8 2.0 - - + +
179B ASN* 4.2 8.1 - - + -
180B ALA* 4.0 30.7 - - + +
183B ALA* 3.2 17.5 - - - +
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LYS 3.8 6.1 - - - +
140B THR* 3.2 6.8 + - - +
142B ALA* 1.3 74.0 - - - +
144B CYS* 1.3 60.4 + - - +
146B ALA* 3.1 5.0 + - - +
147B LYS* 3.0 26.2 + - + +
179B ASN* 3.4 44.2 - - + +
183B ALA* 3.9 7.9 - - + -
119M ASP* 3.9 18.8 - - + +
120M PHE* 3.7 29.4 - - + -
122M TYR* 4.2 18.6 - - + -
124M GLN* 4.9 3.8 - - - +
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Residues in contact with CYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B VAL* 3.3 35.7 - - + +
108B ARG* 5.4 1.1 - - - -
110B MET* 4.8 4.3 - - - -
111B GLY* 3.9 20.9 - - - -
126B LEU* 3.7 23.5 - - + +
140B THR* 3.0 14.5 + - + +
141B ALA* 3.2 9.3 + - - +
143B VAL* 1.3 74.2 - - - +
145B VAL* 1.3 58.8 + - - +
147B LYS* 3.2 11.6 + - + +
148B LEU* 2.9 28.0 + - - +
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 4.5 5.8 - - + -
130B LEU* 3.7 32.3 - - + -
141B ALA 3.0 19.2 + - - +
142B ALA 3.4 9.9 - - - +
143B VAL 3.2 0.4 - - - -
144B CYS* 1.3 76.8 - - - +
146B ALA* 1.3 57.0 + - - +
148B LEU* 3.1 8.6 + - - +
149B HIS* 2.9 25.6 + - - +
156B VAL* 4.4 6.9 - - + +
161B PHE* 4.1 28.0 - - + -
165B LEU* 4.2 14.8 - - + -
187B ILE* 3.9 20.6 - - + -
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Residues in contact with ALA 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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142B ALA 3.8 1.2 + - - -
143B VAL* 3.1 11.1 + - + +
145B VAL* 1.3 75.7 - - - +
147B LYS* 1.3 60.9 + - - +
149B HIS* 3.4 1.9 + - - +
150B ASP* 3.0 29.1 + - - +
183B ALA* 3.7 27.3 - - + +
186B GLU* 4.0 24.8 - - + +
187B ILE* 4.3 11.2 - - + -
120M PHE* 4.0 12.3 - - + -
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Residues in contact with LYS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ARG* 3.2 23.0 + - - +
111B GLY* 3.8 33.3 - - - +
112B CYS* 2.8 32.7 - - - -
143B VAL* 3.0 16.5 + - - +
144B CYS* 3.3 18.8 - - + +
146B ALA* 1.3 76.8 - - - +
148B LEU* 1.3 60.7 + - - +
150B ASP* 3.5 13.0 + - - +
151B ILE* 3.7 16.3 + - - +
21M TYR* 4.5 2.2 - - - +
119M ASP* 4.7 9.6 + - - +
120M PHE* 3.5 55.1 - - + +
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Residues in contact with LEU 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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111B GLY* 5.4 4.7 - - - -
119B THR* 3.8 39.7 - - + +
122B LEU* 5.5 5.2 - - + +
123B CYS* 3.7 25.6 - - - -
126B LEU* 3.8 23.3 - - + -
144B CYS* 2.9 13.7 + - - +
145B VAL* 3.1 8.7 + - - +
147B LYS* 1.3 75.9 - - - +
149B HIS* 1.3 64.8 + - - +
151B ILE* 3.3 4.1 + - + +
152B ASN* 3.3 24.9 + - + +
155B LEU* 5.2 5.2 - - + -
156B VAL* 3.8 15.7 - - + -
161B PHE* 3.8 11.4 - - + -
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Residues in contact with HIS 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 VAL 2.9 15.2 + - - +
146B ALA 3.9 4.0 - - - +
148B LEU* 1.3 74.2 - - - +
150B ASP* 1.3 65.1 + - - +
152B ASN 4.0 2.6 - - - -
153B ALA* 3.8 42.7 + - + +
156B VAL* 3.7 20.6 - - + +
157B GLU* 6.4 0.9 - - + -
162B LEU* 5.1 2.5 - - + -
186B GLU 5.4 0.2 + - - -
187B ILE* 4.2 30.4 - - + +
190B SER* 3.6 32.8 + - - -
191B HIS* 3.0 34.5 + + - -
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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
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114B ARG* 5.7 1.9 - - - +
146B ALA 3.0 16.8 + - - +
147B LYS 3.6 7.9 - - - +
148B LEU 3.2 0.6 - - - -
149B HIS* 1.3 78.7 - - - +
151B ILE* 1.3 68.2 + - - +
186B GLU* 5.3 1.4 - - - +
22M ARG* 4.4 13.9 + - - +
24M ASP* 3.7 29.5 - - - +
120M PHE* 4.1 18.1 - - + -
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Residues in contact with ILE 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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111B GLY* 4.0 15.7 - - - +
113B ILE 3.8 4.7 - - - +
114B ARG* 3.7 44.9 - - + -
116B ASP* 3.3 26.9 - - - +
119B THR* 3.8 30.7 - - + +
147B LYS 3.7 10.7 + - - +
148B LEU* 3.3 7.9 + - + +
149B HIS 3.3 0.4 - - - -
150B ASP* 1.3 86.5 - - - +
152B ASN* 1.3 63.0 + - + +
153B ALA 4.1 1.1 + - - -
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Residues in contact with ASN 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ASP* 5.2 4.6 + - - +
119B THR* 4.6 7.1 + - - +
120B GLU* 5.1 9.1 + - - +
148B LEU 3.3 15.5 + - - +
149B HIS* 4.0 3.5 - - - -
151B ILE* 1.3 84.4 - - + +
153B ALA* 1.3 70.8 + - - +
154B GLN* 4.4 4.7 + - - +
155B LEU* 3.6 45.9 + - + +
156B VAL* 4.0 3.3 - - - +
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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