Contacts of the helix formed by residues 136 - 151 (chain B) in PDB entry 4U2M
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 ARG 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134B PHE* 3.2 1.0 - - - +
135B THR* 1.3 77.9 + - - +
137B HIS* 1.3 64.0 + - - +
138B ALA 3.4 1.8 - - - -
139B SER* 3.4 11.6 + - - -
140B ASP* 3.0 35.5 + - - +
127C THR* 4.2 25.2 + - + +
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Residues in contact with HIS 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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11B LEU* 4.1 5.6 - - + -
45B CYS* 3.8 13.7 - - + -
76B PHE* 3.4 33.4 + + + -
77B MET* 2.9 25.4 + - - -
80B ALA* 3.7 29.2 - - + -
134B PHE* 3.2 27.1 + - + +
135B THR 3.4 0.4 - - - -
136B ARG* 1.3 80.4 - - - +
138B ALA* 1.3 65.3 + - - +
140B ASP* 3.0 13.6 + - + +
141B VAL* 2.9 43.1 + - + +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B SER* 3.6 31.5 - - - +
8B GLN* 3.6 25.1 - - + +
11B LEU* 3.9 19.8 - - + +
80B ALA* 4.9 1.5 - - + +
134B PHE 4.7 0.8 + - - -
135B THR 4.9 4.7 + - - +
136B ARG 3.4 0.4 - - - -
137B HIS* 1.3 79.0 - - - +
139B SER* 1.3 62.9 + - - +
141B VAL* 3.3 6.3 + - - +
142B LEU* 3.1 22.2 + - - +
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Residues in contact with SER 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B SER* 3.0 22.3 + - - -
135B THR 5.4 2.0 + - - -
136B ARG* 3.4 14.1 + - - -
137B HIS 3.2 0.4 - - - -
138B ALA* 1.3 79.2 - - - +
140B ASP* 1.3 57.4 + - - +
142B LEU* 3.4 2.4 + - - +
143B LEU* 2.9 29.2 + - - +
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Residues in contact with ASP 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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136B ARG* 3.0 32.5 + - - +
137B HIS* 3.0 15.5 + - - +
139B SER* 1.3 73.9 - - - +
141B VAL* 1.3 62.0 + - + +
143B LEU* 3.3 12.2 + - - +
144B ASN* 2.9 42.4 + - - +
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Residues in contact with VAL 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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10B VAL* 6.3 0.4 - - + -
11B LEU* 4.5 14.8 - - + -
14B LEU* 4.6 8.3 - - + -
41B VAL* 4.9 7.6 - - + -
44B ALA* 3.9 14.5 - - + +
45B CYS* 3.7 14.4 - - - -
77B MET 4.4 2.9 - - - +
137B HIS* 2.9 48.3 + - + +
138B ALA* 3.6 8.1 - - - +
140B ASP* 1.3 77.0 - - - +
142B LEU* 1.3 57.1 + - - +
144B ASN* 3.3 2.4 + - - +
145B LEU* 2.8 46.9 + - + +
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Residues in contact with LEU 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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6B HIS* 3.8 15.7 - - + -
7B SER* 3.9 16.6 - - - +
10B VAL* 4.1 24.0 - - + -
138B ALA 3.1 16.1 + - - +
139B SER* 3.9 3.8 - - - +
140B ASP 3.3 0.2 - - - -
141B VAL* 1.3 76.8 - - - +
143B LEU* 1.3 62.8 + - - +
145B LEU* 3.2 16.3 + - + +
146B ASN 3.0 18.9 + - - -
172B VAL* 5.1 3.6 - - + -
213B MET 3.6 16.6 - - - +
214B TYR* 3.3 30.0 - - + +
215B THR 4.1 2.5 - - - +
216B SER* 3.7 23.1 - - - +
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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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139B SER 2.9 18.4 + - - +
140B ASP* 3.6 12.3 - - - +
142B LEU* 1.3 76.0 - - - +
144B ASN* 1.3 59.4 - - - +
146B ASN* 3.2 12.8 + - + +
147B ARG* 3.0 66.3 + - + +
214B TYR 5.0 1.8 - - - -
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Residues in contact with ASN 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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44B ALA* 3.0 34.9 + - + +
140B ASP* 2.9 26.7 + - - +
141B VAL 3.8 2.0 - - - +
143B LEU* 1.3 77.7 - - - +
145B LEU* 1.3 60.0 + - - +
147B ARG* 3.2 35.6 + - - +
148B LEU* 2.9 33.3 + - + +
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Residues in contact with LEU 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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10B VAL* 5.2 0.9 - - + -
14B LEU* 4.3 15.3 - - + -
40B ALA* 3.6 40.8 - - + +
41B VAL* 4.5 4.5 - - + +
44B ALA* 4.0 5.4 - - + -
141B VAL* 2.8 38.6 + - + +
142B LEU* 3.2 17.9 + - + +
144B ASN* 1.3 73.2 - - - +
146B ASN* 1.3 58.1 + - - +
148B LEU* 3.3 10.4 + - + +
149B ARG* 2.9 23.2 + - - +
169B HIS* 3.6 11.5 - - - +
172B VAL* 3.8 25.6 - - + -
214B TYR* 3.7 13.0 - - + -
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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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142B LEU 3.0 12.3 + - - +
143B LEU* 3.5 14.9 - - + +
145B LEU* 1.3 73.9 - - - +
147B ARG* 1.3 61.9 + - + +
149B ARG* 2.9 37.6 + - - +
150B SER* 2.8 33.0 + - - -
214B TYR* 3.3 24.6 - - + +
215B THR* 3.6 21.4 - - - +
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Residues in contact with ARG 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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50B LYS* 6.1 2.9 - - - +
143B LEU* 3.0 45.7 + - + +
144B ASN* 3.2 31.9 + - - +
145B LEU 3.3 0.2 - - - -
146B ASN* 1.3 73.4 - - - +
148B LEU* 1.3 69.9 + - + +
149B ARG 3.3 0.2 + - - -
150B SER* 3.3 2.7 + - - -
151B ARG* 3.0 57.2 + - - +
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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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40B ALA* 3.6 28.9 - - - +
43B ALA* 4.0 15.0 - - + +
44B ALA* 4.2 5.6 - - + +
50B LYS* 4.0 29.4 - - + +
144B ASN* 2.9 21.1 + - + +
145B LEU* 3.4 17.7 - - + +
147B ARG* 1.3 80.1 - - + +
149B ARG* 1.3 62.5 + - - +
151B ARG* 3.3 1.4 + - - -
152B ASP 3.0 3.8 + - - -
153B ILE* 2.8 68.3 + - + +
154B LEU* 4.7 1.6 - - + -
169B HIS* 4.0 3.8 - - - +
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Residues in contact with ARG 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 LEU 2.9 14.4 + - - +
146B ASN* 2.9 38.1 + - - +
148B LEU* 1.3 76.6 - - - +
150B SER* 1.3 63.7 + - - +
152B ASP* 3.0 14.6 + - - +
155B THR* 4.4 6.6 - - + +
167B ARG* 3.8 25.2 + - + +
169B HIS* 3.8 14.1 - - + -
210B LEU* 3.5 26.1 - - - +
211B ASP* 3.1 35.0 + - - +
214B TYR* 3.6 34.9 - - + +
215B THR* 5.2 1.2 - - - +
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Residues in contact with SER 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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146B ASN* 2.8 21.3 + - - -
147B ARG* 3.4 11.3 - - - -
149B ARG* 1.3 75.4 - - - +
151B ARG* 1.3 74.6 + - - +
152B ASP* 3.3 1.3 + - - +
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Residues in contact with ARG 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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50B LYS* 5.4 7.3 - - - +
147B ARG* 3.0 55.1 + - - +
148B LEU 3.3 2.0 + - - -
149B ARG 3.2 0.4 - - - -
150B SER* 1.3 88.8 - - - +
152B ASP* 1.3 68.0 + - - +
153B ILE* 3.2 32.5 + - + +
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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