Contacts of the helix formed by residues 155 - 172 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU* 4.4 3.1 - - - +
151A GLU 3.3 19.1 - - - +
152A PRO* 2.3 31.3 + - + +
154A GLN* 1.3 78.9 - - + +
156A GLU* 1.3 64.7 + - - +
157A ARG* 3.7 9.9 + - - +
158A GLY 3.0 12.1 + - - -
159A ARG* 2.9 24.4 + - - +
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Residues in contact with GLU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLN 3.9 1.0 + - - -
155A THR* 1.3 72.0 - - - +
157A ARG* 1.3 65.7 + - + +
159A ARG* 4.1 7.6 - - - +
160A ALA* 3.1 28.5 + - + +
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Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A THR* 4.2 4.4 + - - +
78A LEU* 3.5 30.3 - - + +
79A ASP* 2.6 37.6 + - - -
82A GLU* 2.8 41.8 + - - +
155A THR* 3.1 8.6 - - - +
156A GLU* 1.3 84.2 - - + +
158A GLY* 1.3 56.8 + - - +
160A ALA* 3.8 3.8 - - - +
161A TYR* 3.1 25.8 + - - +
164A ARG* 5.4 0.3 + - - -
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Residues in contact with GLY 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.9 17.7 - - - -
149A TRP* 5.1 0.4 - - - -
152A PRO 3.2 17.7 - - - -
153A ARG* 3.6 10.5 - - - -
155A THR* 3.0 11.3 + - - -
157A ARG* 1.3 74.3 - - - +
159A ARG* 1.3 64.6 + - - +
161A TYR* 3.2 2.8 + - - +
162A TYR* 3.1 28.1 + - - -
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Residues in contact with ARG 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ARG* 2.8 23.7 + - + +
154A GLN* 3.1 37.2 + - - +
155A THR 2.9 13.6 + - - +
156A GLU* 4.1 5.6 - - - +
158A GLY* 1.3 74.7 - - - +
160A ALA* 1.3 57.9 + - - +
162A TYR* 3.5 4.1 + - - +
163A ALA* 3.0 30.0 + - - +
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Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A GLU* 3.1 20.1 + - + +
157A ARG* 3.8 5.8 - - - +
159A ARG* 1.3 77.0 - - - +
161A TYR* 1.3 59.7 + - - +
163A ALA* 3.9 6.4 - - - +
164A ARG* 2.9 43.6 + - - +
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Residues in contact with TYR 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.7 20.9 - - + -
81A VAL* 3.5 27.2 + - + +
82A GLU* 3.9 24.2 - - + +
85A LEU* 3.8 24.6 - - + +
114A TYR* 4.8 2.8 + - - -
149A TRP* 3.7 11.3 - + - -
157A ARG 3.1 17.4 + - - +
158A GLY 3.2 2.9 + - - +
160A ALA* 1.3 76.3 - - - +
162A TYR* 1.3 98.8 + + - +
164A ARG* 3.1 27.0 + - - +
165A PHE* 2.9 50.5 + + - +
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Residues in contact with TYR 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A TRP* 3.2 36.8 + + - -
153A ARG* 3.2 50.7 - - + +
158A GLY 3.1 15.9 + - - +
159A ARG* 4.1 3.6 - - - +
161A TYR* 1.3 109.2 + + - +
163A ALA* 1.3 58.6 + - - +
165A PHE* 3.3 3.1 + + + +
166A GLU* 2.9 31.5 + - - +
177A HIS* 4.0 4.3 - + - +
178A PRO* 3.9 29.6 - - + +
179A ASP* 2.8 36.0 + - - -
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Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ARG 3.0 18.7 + - - +
160A ALA* 3.9 7.0 - - - +
162A TYR* 1.3 76.2 - - - +
164A ARG* 1.3 58.7 + - + +
166A GLU* 3.5 11.1 + - - +
167A ALA* 2.9 30.0 + - - +
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Residues in contact with ARG 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU* 5.0 11.9 + - - +
85A LEU* 4.0 20.2 - - + +
86A ASN* 3.8 29.1 + - - +
89A ILE* 5.5 2.0 - - - +
160A ALA* 2.9 23.9 + - - +
161A TYR* 3.1 40.7 - - - +
163A ALA* 1.3 74.4 - - + +
165A PHE* 1.3 65.1 + - - +
167A ALA* 3.3 5.8 + - - +
168A TRP* 3.0 24.9 + - - +
143B GLU* 3.9 13.7 + - - +
199B HIS* 4.1 3.4 - - + -
202B ARG* 3.8 41.7 - - - +
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Residues in contact with PHE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 3.9 26.6 - - + +
114A TYR* 3.5 35.7 - + - -
161A TYR* 2.9 50.0 + + - +
162A TYR* 3.6 7.6 - + - +
164A ARG* 1.3 74.9 - - - +
166A GLU* 1.3 64.5 + - - +
168A TRP* 3.2 6.8 + + - +
169A LEU* 3.0 29.7 + - + +
178A PRO* 3.5 30.1 - - + -
181A PHE* 3.7 33.9 - + - -
182A ALA* 4.5 4.0 - - + -
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Residues in contact with GLU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A TYR 2.9 17.2 + - - +
163A ALA* 3.7 8.3 - - - +
165A PHE* 1.3 78.0 - - - +
167A ALA* 1.3 59.1 + - - +
169A LEU* 3.2 5.6 + - - +
170A LYS* 2.9 57.9 + - + +
176A GLU 5.6 2.7 - - - +
177A HIS* 5.6 4.4 - - - -
178A PRO* 3.6 20.1 - - + +
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Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ALA 2.9 18.3 + - - +
164A ARG* 3.8 2.2 - - - +
166A GLU* 1.3 79.3 - - - +
168A TRP* 1.3 62.9 + - - +
170A LYS* 3.4 8.1 + - - +
171A GLU* 3.1 24.6 + - - +
199B HIS* 3.4 43.0 + - + +
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Residues in contact with TRP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 3.7 20.0 - - + -
88A ALA* 3.7 32.1 - - + -
89A ILE* 3.5 40.0 + - + +
92A LEU* 3.7 26.2 - - + +
114A TYR* 3.9 18.2 - - + -
115A PRO 4.8 0.4 - - - -
118A VAL* 3.8 16.6 - - + -
164A ARG 3.0 17.0 + - - +
165A PHE* 3.6 12.1 - + - +
166A GLU 3.2 0.2 - - - -
167A ALA* 1.3 76.0 - - - +
169A LEU* 1.3 89.9 + - + +
171A GLU* 3.5 12.8 + - - +
172A ASN* 2.8 42.3 + - - +
181A PHE* 4.4 0.7 - + - -
199B HIS* 3.8 13.6 - - + -
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A VAL* 4.7 1.6 - - + -
165A PHE* 3.0 21.0 + - + +
166A GLU* 3.6 5.8 - - - +
168A TRP* 1.3 87.5 - - + +
170A LYS* 1.3 57.9 + - - +
172A ASN* 2.8 22.8 + - - +
173A GLY 3.2 0.2 + - - -
174A ILE* 3.0 41.4 + - + +
176A GLU 3.5 22.2 - - - +
178A PRO* 3.8 27.4 - - + -
181A PHE* 3.6 50.7 - - + -
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Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A GLU* 2.9 51.3 + - + +
167A ALA* 3.8 7.4 - - - +
169A LEU* 1.3 73.2 - - - +
171A GLU* 1.3 58.7 + - - +
173A GLY 3.0 14.4 + - - -
174A ILE 3.5 12.3 - - - +
175A THR* 5.1 2.9 - - - -
335B ASP 3.3 4.7 - - - +
336B MET* 4.4 4.9 - - + +
339B GLY* 3.0 45.9 - - - +
340B LEU* 4.1 22.7 + - - +
375B ARG* 5.5 4.4 - - - +
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Residues in contact with GLU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ALA 3.1 15.1 + - - +
168A TRP* 3.9 14.0 - - - +
169A LEU 3.3 0.2 - - - -
170A LYS* 1.3 76.2 - - - +
172A ASN* 1.3 63.3 + - - +
173A GLY 3.3 0.9 - - - -
137B TRP* 5.0 4.7 - - - -
198B PRO* 4.0 23.7 - - + +
199B HIS* 3.4 26.3 + - - -
332B GLY* 4.8 1.0 - - - +
335B ASP* 3.3 20.3 - - - +
336B MET* 3.8 20.6 + - - +
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Residues in contact with ASN 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.7 8.2 - - - +
118A VAL* 3.5 23.6 - - + +
122A ARG* 3.0 29.5 + - - -
168A TRP* 2.8 45.2 + - - +
169A LEU* 2.8 11.3 + - - +
171A GLU* 1.3 85.2 + - - +
173A GLY* 1.3 59.9 + - - +
174A ILE* 3.2 15.0 + - + +
335B ASP* 3.0 19.9 - - - +
338B GLN* 5.2 0.5 + - - -
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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