Contacts of the strand formed by residues 167 - 179 (chain A) in PDB entry 1AF6
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 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A SER* 3.4 2.6 - - - -
148A GLU* 2.9 45.8 + - - +
150A GLY 2.8 22.0 - - - +
151A GLY* 3.6 5.6 - - - -
152A SER* 3.1 36.1 - - - +
166A GLU* 1.3 71.7 - - - +
168A ALA* 1.3 69.8 + - - +
169A ASN* 3.1 5.0 + - - +
196A ALA* 3.9 12.6 - - - +
197A ASN 4.8 2.1 + - - -
198A LEU* 4.8 3.6 - - - -
204A LEU* 4.5 3.5 - - + +
250A SER* 3.9 9.4 - - - -
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Residues in contact with ALA 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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145A ARG* 4.0 21.8 - - - +
146A SER 3.6 6.3 - - - -
147A SER* 4.2 5.7 - - - -
166A GLU* 4.1 2.6 + - - +
167A THR* 1.3 75.0 + - - +
169A ASN* 1.3 61.5 + - - +
170A ASP 4.3 0.2 - - - -
196A ALA* 3.6 1.6 - - - -
197A ASN* 2.8 44.4 + - + +
18B GLY* 4.9 0.2 - - - -
19B GLU* 4.3 29.2 + - - +
71B GLN* 4.9 0.4 - - - +
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Residues in contact with ASN 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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145A ARG* 3.7 4.9 - - - -
146A SER* 2.8 40.6 + - - +
148A GLU* 2.8 24.2 + - - +
167A THR* 3.1 18.9 + - - +
168A ALA* 1.3 75.6 - - - +
170A ASP* 1.3 64.2 + - - +
171A VAL* 5.5 1.1 - - - +
195A ARG 3.4 3.6 - - - +
196A ALA* 3.6 13.7 - - - +
247A SER* 2.6 49.6 + - - +
249A GLY 2.9 20.2 - - - +
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Residues in contact with ASP 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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144A THR 3.8 5.6 - - - +
145A ARG* 2.9 35.6 + - - -
169A ASN* 1.3 72.7 - - - +
171A VAL* 1.3 62.3 + - - +
172A PHE* 3.8 24.5 - - + -
193A TYR 3.9 0.7 - - - +
194A GLY* 3.1 4.5 - - - -
195A ARG* 3.0 38.0 + - + +
197A ASN* 2.9 25.7 + - - +
247A SER* 4.5 0.3 - - - -
13B TRP* 2.7 29.5 + - + -
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Residues in contact with VAL 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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122A ILE* 4.1 11.2 - - + -
142A ALA 3.8 0.3 - - - +
143A ALA* 3.3 8.0 - - - +
144A THR* 3.1 42.6 + - - +
146A SER* 5.7 1.1 - - - +
169A ASN 5.5 1.6 - - - +
170A ASP* 1.3 78.6 - - - +
172A PHE* 1.3 68.6 + - - +
173A ASP* 4.6 2.5 - - + -
192A ASP* 3.6 24.2 - - + +
193A TYR 3.4 6.1 - - - +
194A GLY* 4.0 8.1 - - - -
239A MET* 4.5 1.1 - - + -
245A GLY 3.1 29.4 - - - +
246A LEU* 3.9 8.3 - - + -
247A SER 3.8 18.6 - - - +
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Residues in contact with PHE 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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142A ALA 3.7 2.5 - - - +
143A ALA* 4.0 19.5 - - + -
170A ASP* 3.8 32.5 - - + -
171A VAL* 1.3 76.5 - - - +
173A ASP* 1.3 59.9 + - - +
174A VAL* 5.3 3.5 - - + +
191A VAL 3.6 1.6 - - - +
192A ASP* 3.4 5.1 - - - -
193A TYR* 2.8 60.4 + + + +
195A ARG* 4.6 17.7 - - + -
13B TRP* 4.3 15.7 - + - -
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Residues in contact with ASP 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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107A TYR* 3.9 9.2 + - - -
120A TRP* 4.0 2.1 + - - -
122A ILE* 3.6 21.9 - - + +
140A SER 4.7 0.9 - - - +
141A LEU* 3.4 5.4 - - - +
142A ALA* 2.8 41.6 + - - +
171A VAL* 4.6 1.3 - - + -
172A PHE* 1.3 73.1 - - - +
174A VAL* 1.3 65.6 + - - +
175A ARG* 2.9 49.5 + - - +
191A VAL 3.6 1.1 - - - -
192A ASP* 2.4 30.2 - - - +
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Residues in contact with VAL 174 (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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139A LEU* 3.9 17.0 - - + -
140A SER 3.4 2.5 - - - -
141A LEU* 3.8 27.4 - - + -
172A PHE* 5.3 2.7 - - + -
173A ASP* 1.3 80.8 + - - +
175A ARG* 1.3 67.2 + - - +
176A LEU* 6.1 0.2 - - + -
190A GLY* 3.3 2.8 - - - -
191A VAL* 3.0 43.5 + - + +
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Residues in contact with ARG 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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107A TYR* 3.9 15.6 + - - -
108A GLN* 3.0 49.8 + - - +
110A HIS* 3.9 3.6 + - - -
120A TRP* 3.4 54.9 + - + +
122A ILE* 3.7 23.8 - - - +
138A LYS 3.6 0.6 - - - +
139A LEU* 3.3 8.9 - - - +
140A SER* 2.9 40.3 + - - +
173A ASP* 2.9 36.7 + - - +
174A VAL* 1.3 77.6 - - - +
176A LEU* 1.3 60.8 + - - +
177A ALA* 4.1 1.3 - - + +
188A GLU* 3.9 12.8 - - - +
189A LEU 3.3 7.6 - - - +
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A VAL* 4.0 27.1 - - + -
136A PHE* 3.8 13.2 - - + -
137A GLY* 4.4 3.1 - - - -
138A LYS 3.2 18.4 - - - +
139A LEU* 4.4 13.2 - - + +
174A VAL* 6.1 0.4 - - + -
175A ARG* 1.3 73.8 - - - +
177A ALA* 1.3 60.2 + - - +
179A MET* 3.4 35.7 - - + +
187A LEU 4.1 1.6 - - - +
188A GLU* 3.3 2.1 - - - -
189A LEU* 2.8 49.9 + - + +
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Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A GLN* 6.1 0.2 - - - +
137A GLY* 3.3 3.8 - - - -
138A LYS* 2.8 39.5 + - + +
175A ARG* 5.5 0.9 - - + -
176A LEU* 1.3 75.2 - - - +
178A GLN* 1.3 73.5 + - + +
179A MET* 3.3 4.4 - - - +
187A LEU 3.8 4.9 - - - -
188A GLU* 3.6 28.9 - - + +
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Residues in contact with GLN 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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131A ASN* 5.2 1.3 + - - -
136A PHE 4.1 5.6 - - - +
137A GLY* 4.3 3.8 - - - -
138A LYS* 3.3 34.4 - - + +
177A ALA* 1.3 85.4 - - + +
179A MET* 1.3 57.3 + - - +
180A GLU* 2.6 33.1 + - - +
186A THR* 4.5 14.7 - - + -
187A LEU 3.4 6.0 + - - -
188A GLU* 5.0 0.2 - - - +
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Residues in contact with MET 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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136A PHE* 3.3 52.7 - - + +
137A GLY* 4.6 0.2 - - - -
176A LEU* 3.4 31.4 - - + +
177A ALA 4.4 5.8 - - - +
178A GLN* 1.3 75.0 - - - +
180A GLU* 1.3 63.9 + - - +
181A ILE* 3.2 17.4 + - + +
186A THR* 3.4 2.9 - - - -
187A LEU* 3.0 49.5 + - + +
189A LEU* 4.9 9.9 - - + -
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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