Contacts of the helix formed by residues 141 - 159 (chain B) in PDB entry 5IJ0
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 141 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ASN* 4.4 0.2 - - - -
138B SER* 3.8 8.9 + - - -
139B LEU 3.4 4.4 + - - -
140B GLY* 1.3 77.9 - - - +
142B GLY* 1.3 61.7 + - - -
143B THR 3.5 0.2 - - - -
144B GLY* 4.2 1.6 - - - -
145B SER* 2.8 35.1 + - - -
184B ASN* 4.3 1.2 + - - -
501B GDP 3.0 35.2 + - - -
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Residues in contact with GLY 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA* 4.2 7.7 - - - +
99B ASN* 3.7 24.0 - - - +
100B ASN 3.9 11.8 - - - +
101B TRP* 4.3 5.9 - - - +
104B GLY* 5.2 1.6 - - - -
141B GLY* 1.3 72.4 - - - -
143B THR* 1.3 55.7 + - - +
146B GLY* 2.8 30.5 + - - -
184B ASN* 4.4 0.9 - - - -
501B GDP 2.7 18.9 + - - -
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Residues in contact with THR 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLY* 4.1 19.1 - - - +
11B GLN* 3.5 16.2 + - - -
66B VAL* 4.5 1.8 - - + +
67B ASP* 4.2 4.7 - - - -
68B LEU* 3.4 53.0 + - + +
69B GLU* 6.1 0.2 - - - +
96B GLY* 5.3 0.2 - - - -
97B ALA* 4.2 7.2 + - - +
104B GLY* 5.9 1.1 - - - -
142B GLY* 1.3 72.9 - - - +
144B GLY* 1.3 59.3 + - - +
147B MET* 2.7 50.3 + - + +
501B GDP 2.9 11.4 + - - -
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Residues in contact with GLY 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA* 3.8 24.5 - - - -
10B GLY 5.2 0.9 - - - -
11B GLN* 4.0 4.7 + - - -
137B HIS* 4.3 11.4 + - - +
138B SER* 4.1 12.3 - - - -
141B GLY* 3.9 1.9 + - - -
142B GLY 3.5 0.6 - - - -
143B THR* 1.3 78.8 - - - +
145B SER* 1.3 55.8 + - - +
148B GLY* 2.7 32.2 + - - -
501B GDP 3.7 5.3 + - - -
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Residues in contact with SER 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TRP* 3.4 19.5 - - - -
137B HIS* 5.0 2.0 - - - -
138B SER 3.0 17.7 + - - -
139B LEU* 3.7 2.9 - - - -
140B GLY 3.1 16.3 + - - -
141B GLY 2.8 24.9 + - - -
144B GLY* 1.3 75.0 - - - +
146B GLY* 1.3 55.0 + - - +
149B THR* 2.5 37.4 + - - -
184B ASN* 4.4 3.8 - - - -
188B SER* 3.8 17.8 + - - -
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Residues in contact with GLY 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TRP* 3.3 19.6 - - - -
105B HIS* 3.1 31.3 + - - -
142B GLY 2.8 21.0 + - - -
145B SER* 1.3 75.3 - - - +
147B MET* 1.3 56.3 + - - +
149B THR* 3.5 0.2 - - - -
150B LEU* 2.9 25.8 + - - +
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Residues in contact with MET 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 5.5 1.6 - - + -
8B GLN 5.3 0.4 - - - -
9B ALA* 4.0 26.0 - - + +
66B VAL* 3.4 43.7 - - + +
68B LEU* 5.8 4.5 - - + -
104B GLY* 5.2 2.1 - - - -
105B HIS* 4.7 2.6 - - - +
109B GLY* 4.6 26.7 - - - +
112B LEU* 5.4 3.4 - - + -
113B VAL* 4.9 8.7 - - + +
116B VAL* 5.7 0.2 - - - -
135B LEU* 5.6 0.7 - - + -
142B GLY 4.1 0.4 + - - -
143B THR* 2.7 35.8 + - + +
146B GLY* 1.3 68.1 - - - -
148B GLY* 1.3 61.5 + - - +
150B LEU* 3.9 5.1 - - - +
151B LEU* 2.8 58.2 + - + +
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Residues in contact with GLY 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA* 5.4 0.4 - - - -
135B LEU* 3.9 20.9 - - - -
137B HIS* 5.6 1.6 - - - -
144B GLY 2.7 26.2 + - - -
147B MET* 1.3 83.8 - - - +
149B THR* 1.3 55.3 + - - -
151B LEU* 4.5 1.8 - - - -
152B ILE* 2.8 38.9 + - - +
192B LEU* 5.5 1.8 - - - -
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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
----------------------------------------------------------
101B TRP* 3.6 11.8 + - + -
105B HIS* 3.9 14.1 - - + -
145B SER 2.5 27.4 + - - -
146B GLY 3.5 3.8 - - - -
148B GLY* 1.3 75.8 - - - +
150B LEU* 1.3 64.2 + - - +
152B ILE* 3.8 4.0 - - - +
153B SER* 2.9 24.3 + - - -
188B SER* 3.6 20.3 + - - -
191B GLN* 3.2 41.5 - - + +
192B LEU* 4.7 8.2 - - - +
195B ASN* 5.1 0.9 - - - +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B HIS* 3.5 52.3 - - + +
109B GLY* 4.0 4.5 - - - -
110B ALA* 4.0 15.0 - - + +
113B VAL* 3.6 29.4 - - + -
146B GLY 2.9 13.1 + - - +
147B MET* 3.9 3.6 - - - +
149B THR* 1.3 73.3 - - - +
151B LEU* 1.3 59.2 + - - +
153B SER* 3.2 9.4 + - - -
154B LYS* 2.9 52.6 + - + +
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.6 39.0 - - + -
66B VAL* 5.1 0.2 - - + -
113B VAL* 3.5 27.1 - - + +
116B VAL* 4.1 20.4 - - + -
117B LEU* 4.0 12.8 - - + -
120B VAL* 4.9 1.3 - - + -
135B LEU* 5.2 4.0 - - + -
147B MET* 2.8 41.3 + - + +
148B GLY* 3.9 2.7 - - - +
150B LEU* 1.3 74.1 - - - +
152B ILE* 1.3 54.4 + - + +
154B LYS* 3.3 2.2 + - - -
155B VAL* 2.7 55.6 + - + +
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Residues in contact with ILE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 5.6 5.2 - - + -
133B PHE* 5.7 1.3 - - + -
134B GLN 6.0 0.2 - - - -
135B LEU* 3.4 36.3 - - + -
148B GLY 2.8 30.3 + - - +
149B THR 3.8 2.7 - - - +
151B LEU* 1.3 74.7 - - + +
153B SER* 1.3 59.9 + - - +
155B VAL* 3.2 6.6 + - + +
156B ARG* 2.8 29.5 + - - +
164B MET* 3.5 26.2 - - + -
165B ASN 5.4 0.7 - - - +
166B THR* 4.3 8.5 - - + -
192B LEU* 4.4 11.4 - - + -
195B ASN* 4.3 15.3 - - + +
196B THR* 3.7 25.4 - - + -
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Residues in contact with SER 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B HIS* 6.1 0.7 - - - -
149B THR* 2.9 16.0 + - - -
150B LEU* 3.3 14.4 - - - -
152B ILE* 1.3 78.2 - - - +
154B LYS* 1.3 60.0 - - - +
156B ARG* 3.3 3.2 + - - +
157B GLU* 2.8 29.4 + - - +
191B GLN* 4.9 4.7 + - - -
195B ASN* 4.0 33.3 + - - +
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Residues in contact with LYS 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 5.2 3.6 - - + -
117B LEU* 3.8 32.7 - - + +
150B LEU* 2.9 42.5 + - + +
151B LEU* 3.7 5.4 - - - +
153B SER* 1.3 78.9 - - - +
155B VAL* 1.3 57.0 + - - +
157B GLU* 3.2 30.5 + - - +
158B GLU* 2.8 30.1 + - - +
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 4.5 11.7 - - + -
117B LEU* 4.4 9.0 - - + -
120B VAL* 5.1 7.2 - - + -
133B PHE* 3.5 32.5 - - + -
151B LEU* 2.7 50.6 + - + +
152B ILE* 3.2 5.8 + - + +
154B LYS* 1.3 72.9 - - - +
156B ARG* 1.3 52.9 + - - +
158B GLU* 3.4 0.8 + - - -
159B TYR* 2.6 38.4 + - - +
164B MET* 3.4 28.0 - - + -
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Residues in contact with ARG 156 (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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152B ILE 2.8 17.9 + - - +
153B SER* 3.6 5.8 - - - +
155B VAL* 1.3 74.0 - - - +
157B GLU* 1.3 68.0 + - - +
159B TYR 3.7 7.9 - - - -
160B PRO* 2.9 56.0 + - + +
164B MET* 4.1 15.1 - - + +
194B GLU 4.9 3.6 - - - -
195B ASN* 2.3 48.2 + - - +
196B THR 3.7 7.4 + - - -
197B ASP* 2.5 37.6 + - - +
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Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B SER* 2.8 14.8 + - - +
154B LYS* 3.2 44.1 + - - +
156B ARG* 1.3 79.3 - - - +
158B GLU* 1.3 61.6 + - - +
160B PRO* 4.2 5.9 - - - +
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 5.8 3.8 - - + -
121B ARG* 5.4 13.6 - - + -
154B LYS 2.8 15.4 + - - +
155B VAL* 4.6 1.1 - - - -
157B GLU* 1.3 79.0 - - - +
159B TYR* 1.3 98.6 + - + +
160B PRO* 3.2 9.0 - - - +
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Residues in contact with TYR 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 6.1 1.8 - - + -
120B VAL* 4.1 10.5 - - + -
121B ARG* 3.9 17.3 - - + +
124B CYS* 3.1 35.2 - - + +
130B LEU* 4.3 11.2 - - + -
133B PHE* 3.4 28.7 - + + -
155B VAL* 2.6 28.0 + - + +
156B ARG* 3.1 9.8 - - - +
158B GLU* 1.3 105.3 + - + +
160B PRO* 1.3 64.3 - - - +
161B ASP* 3.4 4.3 + - - -
162B ARG* 3.6 29.0 + - + +
164B MET* 4.8 4.3 - - - +
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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