Contacts of the helix formed by residues 136 - 149 (chain B) in PDB entry 1C04
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 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B LEU* 2.4 46.7 - - + +
33B THR 5.2 4.2 - - - +
120B LEU* 5.9 1.7 - - + +
134B GLY 3.5 0.4 - - - -
135B ALA* 1.3 76.7 - - - +
137B LYS* 1.3 62.7 + - - +
138B GLN* 3.0 35.0 + - - +
139B ARG* 3.1 35.6 + - + +
140B VAL* 3.1 26.2 + - - +
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Residues in contact with LYS 137 (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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32B LEU* 4.4 2.6 - - - +
73B ASN* 4.4 24.0 + - + +
82B TYR* 3.5 45.5 - - + +
83B GLU* 3.2 36.6 + - - +
84B LYS* 4.7 9.3 - - - +
135B ALA 3.7 4.9 + - - -
136B ASP* 1.3 70.9 + - - +
138B GLN* 1.3 59.2 + - - +
140B VAL* 3.6 7.4 + - + +
141B GLY* 3.0 25.3 + - - +
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Residues in contact with GLN 138 (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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34B ARG* 5.4 16.8 + - - +
136B ASP* 3.0 11.3 + - - +
137B LYS* 1.3 78.2 - - - +
139B ARG* 1.3 65.2 + - + +
141B GLY* 3.2 2.3 + - - -
142B GLU* 2.9 35.9 + - + +
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Residues in contact with ARG 139 (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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32B LEU* 5.4 0.6 - - - +
117B GLU* 3.2 28.1 - - - +
118B GLU 2.7 29.7 + - - +
119B GLY* 4.1 8.1 - - - -
120B LEU* 3.9 28.0 - - + +
136B ASP* 3.1 34.1 + - + +
138B GLN* 1.3 83.0 - - + +
140B VAL* 1.3 57.1 + - - +
142B GLU* 3.5 18.2 + - - +
143B LEU* 3.1 29.5 + - - +
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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
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82B TYR* 4.2 4.9 - - + +
83B GLU* 4.1 6.5 - - - -
84B LYS* 4.0 19.1 - - + +
120B LEU* 4.1 9.2 - - + -
132B VAL* 3.6 31.0 - - - +
133B LYS 4.0 2.2 - - - -
134B GLY* 3.5 36.3 - - - +
136B ASP 3.1 22.2 + - - +
137B LYS* 3.7 11.7 - - + +
139B ARG* 1.3 75.3 - - - +
141B GLY* 1.3 66.0 + - - +
143B LEU* 3.5 0.5 + - - -
144B ALA* 3.2 23.6 + - - +
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Residues in contact with GLY 141 (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 LYS* 5.4 7.6 - - - -
137B LYS* 3.0 17.6 + - - -
138B GLN* 3.6 3.6 - - - -
140B VAL* 1.3 79.5 - - - +
142B GLU* 1.3 56.1 + - - +
144B ALA* 3.6 5.0 + - - +
145B ALA* 3.1 27.5 + - - +
163B TYR* 5.0 1.6 + - - -
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Residues in contact with GLU 142 (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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138B GLN* 2.9 25.6 + - + +
139B ARG* 3.9 19.1 + - - +
141B GLY* 1.3 73.3 - - - +
143B LEU* 1.3 64.5 + - - +
145B ALA* 3.4 6.6 + - - +
146B ASN* 3.0 44.6 + - - +
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Residues in contact with LEU 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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114B ILE* 4.3 16.2 - - + -
115B GLU 5.7 0.2 - - - +
116B PRO* 4.2 13.2 - - + -
120B LEU* 3.9 23.3 - - + -
122B ILE* 4.1 22.9 - - + -
132B VAL* 3.8 21.5 - - + -
139B ARG 3.1 17.9 + - - +
140B VAL 3.5 2.4 + - - +
142B GLU* 1.3 75.8 - - - +
144B ALA* 1.3 60.5 + - - +
146B ASN* 3.1 12.0 + - + +
147B ILE* 2.9 43.0 + - + +
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Residues in contact with ALA 144 (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 LYS* 3.8 26.5 - - + -
86B LEU* 3.7 18.0 - - + +
132B VAL* 4.0 20.1 - - + +
140B VAL 3.2 18.3 + - - +
141B GLY 3.9 3.8 - - - +
143B LEU* 1.3 77.2 - - - +
145B ALA* 1.3 57.4 + - - +
147B ILE* 3.4 1.0 + - - +
148B ARG* 3.1 27.7 + - - +
163B TYR* 4.2 7.2 - - + -
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Residues in contact with ALA 145 (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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141B GLY 3.1 16.7 + - - +
142B GLU* 3.8 7.9 - - - +
143B LEU 3.2 0.4 - - - -
144B ALA* 1.3 75.1 - - - +
146B ASN* 1.3 61.4 + - - +
148B ARG* 3.6 3.4 + - - +
149B ALA* 3.1 28.8 + - - +
163B TYR* 3.4 23.7 + - - +
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Residues in contact with ASN 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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114B ILE* 5.0 2.5 - - + +
142B GLU* 3.0 35.1 + - - +
143B LEU* 3.1 17.9 + - + +
145B ALA* 1.3 80.0 + - - +
147B ILE* 1.3 64.9 + - - +
149B ALA* 3.5 14.6 + - - +
150B VAL* 3.6 14.0 + - - +
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Residues in contact with ILE 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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86B LEU* 3.8 17.7 - - + -
102B LEU* 3.7 31.0 - - + -
104B LEU* 4.4 9.9 - - + -
114B ILE* 4.0 14.1 - - + -
122B ILE* 4.3 10.8 - - + -
130B ILE* 4.2 14.6 - - + -
132B VAL* 4.1 23.6 - - + -
143B LEU* 2.9 32.4 + - + +
144B ALA 3.8 4.7 - - - +
146B ASN* 1.3 75.0 - - - +
148B ARG* 1.3 65.7 + - - +
150B VAL* 2.9 27.4 + - - +
161B ILE* 3.5 9.1 - - + +
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Residues in contact with ARG 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 3.9 9.8 - - + +
144B ALA 3.1 17.0 + - - +
145B ALA 3.8 4.2 + - - +
146B ASN 3.4 0.2 - - - -
147B ILE* 1.3 77.6 - - - +
149B ALA* 1.3 60.8 + - - +
150B VAL 3.1 1.1 + - - -
151B ARG 3.2 4.7 + - - +
152B PRO* 3.1 39.3 - - + +
153B PRO* 3.6 16.3 - - - +
161B ILE* 3.6 28.6 + - - +
163B TYR* 3.6 34.3 + - - +
166B GLU* 2.7 39.6 + - - -
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Residues in contact with ALA 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 ALA 3.1 19.1 + - - +
146B ASN* 3.7 13.7 - - - +
147B ILE 3.1 0.4 - - - -
148B ARG* 1.3 76.0 - - - +
150B VAL* 1.3 65.2 + - - +
151B ARG 3.2 0.6 + - - -
152B PRO* 3.7 17.7 - - + +
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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
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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