Contacts of the helix formed by residues 170 - 184 (chain A) in PDB entry 2AF0
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 PHE 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A PHE* 4.2 10.8 - + + -
116A CYS* 3.6 22.0 - - + -
119A PHE* 3.6 37.7 - + + -
132A ALA* 3.6 24.0 - - + -
135A ILE* 3.2 51.6 - - + -
136A TYR 4.5 2.0 - - - -
140A ILE* 4.2 6.1 - - + -
158A ILE* 3.8 33.9 - - + -
167A SER 4.8 1.6 + - - -
168A GLY* 3.2 0.6 - - - -
169A CYS* 1.3 83.1 - - + +
171A THR* 1.3 54.9 + - - +
172A THR 3.4 1.8 - - - -
173A ALA* 3.3 6.7 + - - +
174A GLN* 2.7 37.9 + - - +
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Residues in contact with THR 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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120A LYS* 5.4 8.7 - - + -
167A SER 4.3 4.7 - - - +
168A GLY* 3.1 36.4 + - - -
169A CYS 3.6 0.2 - - - -
170A PHE* 1.3 77.3 - - - +
172A THR* 1.3 72.5 + - - +
174A GLN* 3.1 10.6 + - - +
175A LYS* 2.9 28.2 + - - +
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Residues in contact with THR 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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154A THR* 4.0 22.9 - - - +
169A CYS 5.3 0.6 + - - -
170A PHE 3.4 0.4 - - - -
171A THR* 1.3 82.8 + - - +
173A ALA* 1.3 63.2 + - - +
175A LYS* 3.5 4.4 + - - +
176A ARG* 3.2 20.5 + - + +
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Residues in contact with ALA 173 (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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112A PHE* 3.9 19.7 - - + -
148A ILE* 4.6 0.2 - - + -
150A ILE* 4.1 27.7 - - + +
154A THR* 5.4 3.6 - - - -
158A ILE* 4.2 23.6 - - + -
170A PHE 3.3 7.0 + - - +
171A THR 3.2 0.4 - - - -
172A THR* 1.3 79.7 - - - +
174A GLN* 1.3 63.1 + - - +
176A ARG* 3.5 3.9 + - - +
177A VAL* 3.1 27.2 + - - +
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Residues in contact with GLN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 3.9 9.2 - - - -
113A TRP* 3.4 46.3 + - + +
116A CYS* 3.5 22.1 - - + +
117A GLU* 3.1 22.5 + - - -
120A LYS* 3.5 25.5 + - - +
170A PHE 2.7 23.7 + - - +
171A THR* 3.1 10.1 + - - +
173A ALA* 1.3 72.6 - - - +
175A LYS* 1.3 56.1 - - - +
177A VAL* 3.1 2.8 + - - +
178A TYR* 2.6 34.9 + - + +
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Residues in contact with LYS 175 (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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171A THR* 2.9 17.0 + - - +
172A THR* 4.0 4.3 - - - +
174A GLN* 1.3 75.2 - - - +
176A ARG* 1.3 62.5 + - - +
178A TYR* 3.6 7.3 - - + +
179A SER* 2.9 43.3 + - - +
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Residues in contact with ARG 176 (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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109A ASN* 5.5 3.8 - - - +
149A ASN* 3.3 43.1 + - - +
150A ILE* 4.7 10.6 - - + +
151A ASP* 5.6 5.5 + - - +
172A THR* 3.2 12.0 + - + +
173A ALA* 3.6 10.3 - - - +
175A LYS* 1.3 79.7 - - - +
177A VAL* 1.3 61.4 + - - +
179A SER* 3.4 4.1 + - - -
180A LEU* 2.8 57.6 + - - +
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Residues in contact with VAL 177 (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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109A ASN* 3.2 53.6 - - + +
112A PHE* 3.7 23.3 - - + -
113A TRP* 4.4 3.8 - - + -
148A ILE* 4.1 13.0 - - + -
149A ASN 5.6 1.1 - - - +
150A ILE* 5.3 1.1 - - + -
173A ALA 3.1 17.0 + - - +
174A GLN 3.1 3.8 + - - +
176A ARG* 1.3 87.1 - - - +
178A TYR* 1.3 65.4 + - - +
180A LEU* 3.3 7.8 + - - +
181A MET* 3.0 29.7 + - + +
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Residues in contact with TYR 178 (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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84A PHE* 3.5 32.0 - + - +
85A ASP* 2.6 28.8 + - - -
88A LEU* 4.0 12.8 - - + -
113A TRP* 3.3 31.2 - + - +
174A GLN* 2.6 21.3 + - + +
175A LYS* 3.6 9.9 - - + +
177A VAL* 1.3 73.7 - - - +
179A SER* 1.3 57.3 + - - +
181A MET* 3.1 12.3 + - - +
182A GLU* 2.7 63.2 + - + +
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Residues in contact with SER 179 (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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175A LYS* 2.9 30.8 + - - +
176A ARG* 3.9 4.3 - - - -
178A TYR* 1.3 81.6 - - - +
180A LEU* 1.3 62.9 + - - +
182A GLU* 4.2 5.5 + - - -
183A ASN* 2.7 39.5 + - - +
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Residues in contact with LEU 180 (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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109A ASN* 4.1 21.1 - - - +
176A ARG* 2.8 40.7 + - - +
177A VAL* 3.3 14.1 - - - +
178A TYR 3.1 0.2 - - - -
179A SER* 1.3 75.7 - - - +
181A MET* 1.3 64.1 + - + +
183A ASN* 4.6 0.2 - - - +
184A ASN* 2.8 56.5 + - + +
185A SER* 4.6 6.1 - - - +
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Residues in contact with MET 181 (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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84A PHE* 3.5 21.1 - - + -
88A LEU* 5.6 0.2 - - + -
97A PHE* 4.0 7.0 - - + -
101A LEU* 4.8 2.2 - - + -
109A ASN* 3.9 13.2 - - + -
110A ILE* 3.7 44.6 - - + -
113A TRP* 3.7 40.2 - - + -
177A VAL* 3.0 19.1 + - + +
178A TYR* 3.6 5.8 - - - +
180A LEU* 1.3 81.7 - - + +
182A GLU* 1.3 61.9 + - - +
185A SER* 3.1 23.8 + - - +
186A TYR* 2.9 28.2 + - - +
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Residues in contact with GLU 182 (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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84A PHE* 3.6 33.4 - - + +
85A ASP* 5.4 0.7 - - - +
178A TYR* 2.7 46.4 + - + +
179A SER* 3.9 4.8 + - - +
181A MET* 1.3 73.8 - - - +
183A ASN* 1.3 73.6 + - - +
186A TYR* 3.7 8.3 - - + -
187A PRO* 3.3 19.2 - - - +
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Residues in contact with ASN 183 (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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179A SER* 2.7 36.3 + - - +
180A LEU 4.6 0.4 - - - +
182A GLU* 1.3 89.0 + - - +
184A ASN* 1.3 58.9 + - + +
187A PRO* 3.8 13.3 - - - +
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Residues in contact with ASN 184 (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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180A LEU* 2.8 38.5 + - + +
181A MET 3.3 1.4 + - - -
183A ASN* 1.3 80.5 - - + +
185A SER* 1.3 66.3 + - - +
186A TYR 3.3 1.6 + - - -
187A PRO* 3.4 11.4 - - - +
188A ARG* 3.1 42.0 + - - +
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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