Contacts of the helix formed by residues 155 - 172 (chain B) in PDB entry 4M83
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 THR 155 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LEU* 3.9 6.4 - - + +
151B GLU 3.8 12.6 - - - +
152B PRO* 2.9 18.6 + - + +
154B GLN* 1.3 79.7 - - - +
156B GLU* 1.3 59.8 + - - +
157B ARG* 3.6 8.9 + - - +
158B GLY* 2.8 21.3 + - - -
159B ARG* 2.8 31.8 + - - +
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Residues in contact with GLU 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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154B GLN 4.1 2.9 - - - +
155B THR* 1.3 74.0 - - - +
157B ARG* 1.3 53.8 + - - +
159B ARG* 2.3 45.3 + - - +
160B ALA* 2.8 35.5 + - - +
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Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B THR* 5.4 0.8 + - - -
78B LEU* 3.5 38.9 + - + +
79B ASP* 3.1 29.9 + - - +
82B GLU* 3.0 32.7 + - - +
83B PRO* 5.7 0.8 - - - +
155B THR* 3.2 7.8 - - - +
156B GLU* 1.3 78.4 - - - +
158B GLY* 1.3 51.7 + - - +
160B ALA* 3.2 6.7 + - - +
161B TYR* 2.6 34.3 + - - +
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Residues in contact with GLY 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 3.9 12.1 - - - +
149B TRP* 5.1 1.1 - - - -
152B PRO 3.7 12.8 - - - -
153B ARG* 4.5 4.7 - - - -
155B THR* 2.8 20.8 + - - -
157B ARG* 1.3 72.2 - - - +
159B ARG* 1.3 64.6 + - - +
161B TYR* 3.3 9.7 - - - +
162B TYR* 3.0 32.1 + - - -
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Residues in contact with ARG 159 (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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153B ARG 3.5 13.6 + - - +
154B GLN* 3.0 48.9 + - - +
155B THR 2.8 19.7 + - - +
156B GLU* 2.3 52.2 + - - +
158B GLY* 1.3 77.1 - - - +
160B ALA* 1.3 57.2 + - - +
162B TYR* 4.0 4.2 - - - +
163B ALA* 3.0 26.0 + - - +
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Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU* 5.4 0.2 - - - -
156B GLU 2.8 22.1 + - - +
157B ARG* 3.6 5.8 - - - +
159B ARG* 1.3 71.1 - - - +
161B TYR* 1.3 62.4 + - - +
163B ALA* 3.2 8.4 - - - +
164B ARG* 2.9 30.5 + - - +
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Residues in contact with TYR 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 3.9 9.0 - - + -
81B VAL* 3.4 25.3 + - + +
82B GLU* 3.9 36.3 + - + +
85B LEU* 3.6 33.7 - - + +
114B TYR* 4.7 4.2 + - - -
149B TRP* 3.4 36.2 - + - -
157B ARG 2.6 18.1 + - - +
158B GLY* 3.2 11.6 + - - +
160B ALA* 1.3 73.0 - - - +
162B TYR* 1.3 86.2 + + - +
163B ALA 3.0 1.2 + - - -
164B ARG* 3.2 10.9 + - - +
165B PHE* 3.2 31.4 + + - +
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Residues in contact with TYR 162 (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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149B TRP* 3.5 45.3 + + - +
153B ARG* 3.2 32.1 + - + -
158B GLY 3.0 23.7 + - - +
159B ARG* 4.2 3.8 - - - +
161B TYR* 1.3 86.4 - + - +
163B ALA* 1.3 61.2 + - - +
165B PHE* 3.5 7.0 + + - +
166B GLU* 3.1 31.8 + - + +
177B HIS* 3.4 33.7 - + - -
178B PRO* 4.4 15.9 - - + -
179B ASP* 2.8 31.0 + - - -
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Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ARG 3.0 20.3 + - - +
160B ALA* 3.2 12.8 - - - +
161B TYR 3.0 0.8 - - - -
162B TYR* 1.3 76.4 - - - +
164B ARG* 1.3 67.0 + - - +
165B PHE 3.4 0.3 + - - -
166B GLU* 3.5 10.2 + - - +
167B ALA* 3.5 14.0 + - - +
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Residues in contact with ARG 164 (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 GLU* 5.8 0.4 + - - -
85B LEU* 4.4 6.3 - - + -
86B ASN* 2.8 49.6 + - - +
89B ILE* 3.7 26.0 - - + +
160B ALA 2.9 14.2 + - - +
161B TYR* 3.2 5.1 + - - +
163B ALA* 1.3 76.3 - - - +
165B PHE* 1.3 63.3 + - - +
167B ALA* 3.6 3.6 + - - +
168B TRP* 3.2 21.8 + - - +
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Residues in contact with PHE 165 (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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85B LEU* 4.0 30.2 - - + +
114B TYR* 4.3 25.6 - + - -
161B TYR* 3.2 34.4 + + - +
162B TYR* 3.7 11.4 - + - +
164B ARG* 1.3 79.9 - - - +
166B GLU* 1.3 62.5 + - - +
168B TRP* 3.3 15.8 + + - +
169B LEU* 3.3 24.9 + - + +
178B PRO* 3.5 36.6 - - + -
181B PHE* 3.6 38.6 - + - -
182B ALA* 4.5 4.0 - - + -
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Residues in contact with GLU 166 (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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162B TYR* 3.1 22.0 + - + +
163B ALA* 3.9 5.8 - - - +
164B ARG 3.4 0.2 - - - -
165B PHE* 1.3 76.9 - - - +
167B ALA* 1.3 62.2 + - - +
169B LEU* 3.3 8.6 + - - +
170B LYS* 3.3 18.8 + - - +
174B ILE 5.0 0.2 - - - +
177B HIS* 3.6 26.4 + - - -
178B PRO* 4.0 18.8 - - + -
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Residues in contact with ALA 167 (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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163B ALA 3.5 12.8 + - - +
164B ARG* 4.2 4.0 - - - +
165B PHE 3.4 0.4 - - - -
166B GLU* 1.3 79.7 - - - +
168B TRP* 1.3 62.8 + - - +
170B LYS* 3.3 8.2 + - - +
171B GLU* 3.1 34.9 + - + +
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Residues in contact with TRP 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 4.3 6.5 - - + -
88B ALA* 3.6 30.5 - - + -
89B ILE* 3.4 37.7 - - + +
92B LEU* 3.5 40.6 - - + +
114B TYR* 4.1 7.6 - - + -
115B PRO* 5.2 0.7 - - + -
118B VAL* 3.5 24.2 - - + -
164B ARG 3.2 16.5 + - - +
165B PHE* 3.6 17.5 - + - +
166B GLU 3.2 0.4 - - - -
167B ALA* 1.3 79.4 - - - +
169B LEU* 1.3 81.8 + - + +
171B GLU* 3.4 26.3 + - - +
172B ASN* 2.8 41.6 + - - +
181B PHE* 4.1 11.9 - + - -
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Residues in contact with LEU 169 (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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118B VAL* 4.8 0.2 - - + -
165B PHE* 3.3 18.0 + - + +
166B GLU* 3.7 7.0 - - - +
167B ALA 3.3 0.2 - - - -
168B TRP* 1.3 95.5 - - + +
170B LYS* 1.3 57.1 + - - +
172B ASN* 3.1 8.7 + - - +
174B ILE* 2.7 65.9 + - + +
175B THR 5.3 0.2 - - - -
176B GLU 3.3 25.1 - - - +
178B PRO* 4.1 16.2 - - + -
181B PHE* 3.8 41.7 - - + -
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Residues in contact with LYS 170 (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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166B GLU 3.3 9.6 + - - +
167B ALA* 3.3 12.0 + - - +
168B TRP 3.2 0.4 - - - -
169B LEU* 1.3 76.5 - - - +
171B GLU* 1.3 66.5 + - - +
173B GLY* 3.3 9.8 + - - -
174B ILE 3.3 8.0 + - - +
175B THR* 5.6 8.5 - - + +
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Residues in contact with GLU 171 (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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92B LEU* 6.1 0.3 - - - +
167B ALA* 3.1 28.3 + - + +
168B TRP* 3.5 29.0 - - - +
170B LYS* 1.3 77.2 - - - +
172B ASN* 1.3 63.0 + - - +
173B GLY 3.0 5.9 + - - -
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Residues in contact with ASN 172 (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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92B LEU* 3.2 12.4 - - - +
118B VAL* 3.5 24.1 - - + +
121B ARG* 5.8 1.0 - - - +
122B ARG* 2.9 38.2 + - - +
168B TRP* 2.8 48.1 + - - +
169B LEU* 3.1 8.2 + - - +
171B GLU* 1.3 80.5 + - - +
173B GLY* 1.3 65.0 + - - +
174B ILE* 3.2 11.4 + - + +
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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