Contacts of the strand formed by residues 167 - 179 (chain A) in PDB entry 1I9R
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 GLY 167 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ARG 3.6 0.4 + - - -
166A GLN* 1.3 79.0 - - - +
168A LEU* 1.3 60.9 + - - -
169A TYR* 3.2 10.6 - - - -
230A GLU* 2.9 14.8 - - - +
231A LEU 2.5 43.2 + - - -
260A LYS* 4.4 4.9 - - - -
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Residues in contact with LEU 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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167A GLY* 1.3 73.2 - - - -
169A TYR* 1.3 66.9 + - - +
228A VAL* 3.4 20.2 - - + -
229A PHE* 3.0 25.6 - - - +
230A GLU* 3.4 28.9 - - + +
260A LYS* 3.6 6.4 - - - +
261A LEU* 3.5 34.7 + - + +
121C GLN* 4.8 22.2 - - + +
123C ALA* 4.6 8.1 - - + -
147C THR* 4.1 12.1 - - + -
149C SER* 4.7 19.7 - - - -
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Residues in contact with TYR 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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122A ILE* 4.2 7.8 - - + +
152A LEU 5.2 1.0 + - - -
163A VAL* 3.7 26.8 - - + +
165A ARG* 2.4 38.2 + - - +
167A GLY* 3.2 31.2 - - - -
168A LEU* 1.3 83.4 - - - +
170A TYR* 1.3 61.8 + - - +
171A ILE* 3.7 18.1 + - + +
228A VAL* 3.3 5.2 - - - -
229A PHE* 2.6 32.3 + - - +
231A LEU* 3.7 23.8 - - + -
258A LEU* 3.6 21.5 - - + -
259A LEU 3.2 7.0 - - - +
260A LYS* 3.4 41.4 - - + +
261A LEU* 4.5 3.6 - - - -
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Residues in contact with TYR 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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169A TYR* 1.3 72.5 - - - +
171A ILE* 1.3 59.1 + - - +
172A TYR* 4.1 17.9 - + + +
224A HIS* 4.6 0.7 + - - -
226A GLY* 3.2 20.3 + - - -
227A GLY* 3.1 31.2 - - - -
228A VAL* 4.1 14.6 - - + -
257A GLY 4.2 0.2 - - - +
258A LEU* 3.2 4.0 - - - -
259A LEU* 2.7 62.3 + - + +
261A LEU* 4.2 4.8 - - + +
170B TYR* 3.8 33.4 + + - -
170C TYR* 3.8 29.3 + + - -
172C TYR* 4.4 5.0 - + - -
224C HIS* 4.0 9.2 + - - -
259C LEU* 4.1 11.7 - - + -
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Residues in contact with ILE 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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169A TYR* 4.2 9.2 - - + +
170A TYR* 1.3 78.9 - - - +
172A TYR* 1.3 66.8 + - - +
193A LEU* 3.1 36.8 - - + -
205A LEU* 4.8 2.0 - - + -
206A LEU* 4.5 1.6 - - - +
225A LEU 3.3 0.7 - - - +
226A GLY* 2.7 29.6 - - - -
227A GLY 3.1 11.1 + - - +
229A PHE* 4.1 19.3 - - + -
231A LEU* 3.7 34.8 - - + -
237A VAL* 4.3 20.6 - - + -
256A PHE* 4.6 2.9 - - + -
257A GLY 3.8 7.0 - - - +
258A LEU* 3.7 15.9 - - + -
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Residues in contact with TYR 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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124A ALA 3.9 1.9 + - - -
125A HIS* 2.7 38.5 + + - +
170A TYR* 4.1 23.1 - + + +
171A ILE* 1.3 79.8 - - - +
173A ALA* 1.3 67.8 + - - +
174A GLN* 4.8 3.4 - - + -
193A LEU* 5.3 0.9 - - - -
224A HIS* 4.5 12.1 - + - +
225A LEU* 2.8 14.4 - - - +
226A GLY* 4.1 5.6 - - - -
255A SER* 5.3 0.9 - - - -
256A PHE* 3.3 8.4 - - - -
257A GLY* 2.8 72.2 + - - +
258A LEU* 3.8 4.7 - - - -
259A LEU* 4.9 2.0 - - + -
170B TYR* 4.6 2.9 - + - -
226B GLY 4.4 2.5 - - - -
227B GLY* 3.2 29.4 - - - -
228B VAL* 2.8 26.2 + - + +
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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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172A TYR* 1.3 81.7 - - - +
174A GLN* 1.3 61.9 + - - +
175A VAL* 3.9 3.4 + - + -
193A LEU* 5.1 2.0 - - + -
223A ILE* 3.9 1.2 - - - +
224A HIS* 3.6 3.0 - - - -
225A LEU* 3.1 45.9 + - + +
239A VAL* 3.7 33.7 - - + -
255A SER 3.4 10.1 - - - +
256A PHE* 4.0 2.5 - - + +
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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
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172A TYR* 4.8 3.8 - - + -
173A ALA* 1.3 73.5 - - - +
175A VAL* 1.3 67.8 + - - +
176A THR* 3.6 11.3 - - - +
222A SER* 4.1 4.8 + - - -
223A ILE 3.3 8.4 + - - +
224A HIS* 3.3 28.9 - - + +
252A GLY 5.2 1.6 - - - -
253A PHE 2.6 29.5 + - - -
254A THR* 3.3 1.0 - - - -
255A SER* 2.8 50.1 + - - +
206B LEU* 5.5 3.1 - - + -
207B ARG 3.4 13.7 - - - +
208B ALA* 3.6 5.7 - - - +
224B HIS 3.6 6.8 - - - +
225B LEU* 3.5 27.4 - - + +
226B GLY 4.9 2.0 - - - +
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Residues in contact with VAL 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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138A LEU* 4.0 16.8 - - + -
140A TRP* 4.6 3.1 - - + -
173A ALA* 3.9 4.0 + - + -
174A GLN* 1.3 83.0 - - - +
176A THR* 1.3 70.9 + - - +
177A PHE* 4.6 1.1 - - + -
189A PHE* 4.3 27.6 - - + -
191A ALA* 4.9 4.0 - - + -
221A GLN 4.1 0.2 - - - +
222A SER 3.3 0.3 - - - -
223A ILE* 2.5 58.8 + - + +
225A LEU* 6.5 0.2 - - + -
239A VAL* 4.3 12.8 - - + -
241A VAL* 4.9 3.6 - - + -
247A VAL* 4.6 7.6 - - + -
254A THR* 3.8 17.7 - - + +
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Residues in contact with THR 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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174A GLN* 3.6 2.9 - - - +
175A VAL* 1.3 78.9 - - - +
177A PHE* 1.3 64.7 + - - +
220A GLN* 3.9 7.8 + - - +
221A GLN 3.0 9.7 + - - -
222A SER* 2.9 24.0 - - - +
247A VAL* 3.7 2.3 - - - -
248A SER* 2.8 30.5 + - - -
253A PHE* 2.9 63.2 - - + +
254A THR* 3.2 8.0 + - - -
207B ARG 3.9 0.4 - - - +
209B ALA 4.9 0.2 + - - -
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Residues in contact with PHE 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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175A VAL 4.6 4.3 - - - -
176A THR* 1.3 77.9 + - - +
178A CYS* 1.3 63.7 + - - +
179A SER* 3.7 25.1 - - - -
189A PHE* 3.3 67.5 - + + -
210A ASN* 4.1 9.2 - - + -
212A HIS* 3.9 3.8 - + - -
219A GLY 5.5 0.4 - - - -
220A GLN* 3.0 4.5 - - - +
221A GLN* 2.8 72.1 + - + +
223A ILE* 4.2 13.7 - - + -
246A GLN* 3.3 15.3 - - + +
247A VAL* 3.6 8.1 - - - -
248A SER* 3.6 7.9 - - - +
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Residues in contact with CYS 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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177A PHE* 1.3 73.8 - - - +
179A SER* 1.3 61.8 + - - +
218A CYS* 2.0 56.1 - - - -
219A GLY 3.7 1.6 - - - -
220A GLN* 3.6 19.7 - - + -
246A GLN* 2.9 15.8 + - - +
248A SER* 3.9 10.5 + - - +
55H ASN* 2.4 37.4 - - - +
57H ASP* 3.9 7.4 - - - -
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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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177A PHE* 3.7 11.4 - - - -
178A CYS* 1.3 76.4 - - - +
180A ASN* 1.3 62.5 + - - +
184A SER* 6.0 1.6 - - - -
212A HIS* 2.8 38.6 - - - +
213A SER* 4.2 5.4 + - - +
215A ALA 3.7 0.3 - - - +
218A CYS* 2.8 13.3 - - - +
219A GLY 2.7 35.6 + - - +
246A GLN* 3.6 20.2 - - - +
55H ASN* 4.2 0.7 - - - -
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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