Contacts of the strand formed by residues 181 - 189 (chain M) in PDB entry 7K60
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 TYR 181 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92C GLU* 6.0 0.9 - - - -
104D GLY* 5.3 2.9 - - - -
105D GLU* 2.9 45.6 + - + +
176M TYR* 3.3 26.2 - + + +
177M THR* 3.4 22.8 - - + +
178M PHE 3.5 7.6 + - - +
179M THR 3.4 0.4 - - - -
180M SER* 1.3 85.7 - - - +
182M THR* 1.3 64.3 + - - +
183M ILE* 4.4 3.6 - - - +
201M TYR* 4.3 0.9 - - - -
202M PRO* 3.3 19.2 - - - +
247M ARG* 3.4 58.0 + - + -
248M LYS 3.9 3.1 - - - +
249M SER* 3.6 22.4 - - - +
257M ASP* 4.5 1.8 - - - -
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Residues in contact with THR 182 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180M SER 4.2 0.2 + - - -
181M TYR* 1.3 75.1 - - - +
183M ILE* 1.3 61.1 + - - +
184M GLN* 3.1 26.0 + - - +
199M TYR* 4.4 13.5 - - + -
200M ILE 3.3 11.9 - - - -
201M TYR* 3.5 31.0 - - + -
247M ARG* 3.6 3.8 - - - -
248M LYS* 2.5 50.7 + - - +
249M SER 4.7 0.4 + - - +
250M SER* 4.6 14.1 - - - +
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Residues in contact with ILE 183 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153M LEU* 4.7 5.8 - - + -
171M CYS* 3.9 28.5 - - - -
173M ALA* 4.9 2.7 - - + -
176M TYR* 3.3 26.9 - - - +
178M PHE* 4.7 6.5 - - + -
181M TYR 4.4 5.2 - - - +
182M THR* 1.3 79.1 - - - +
184M GLN* 1.3 63.0 + - - +
185M TRP* 4.0 20.9 - - - +
198M GLY 4.1 0.2 - - - +
199M TYR* 3.2 4.9 - - - -
200M ILE* 3.0 41.5 + - + +
202M PRO* 4.8 1.3 - - + -
228M VAL* 3.9 18.8 - - + -
245M CYS* 4.0 10.8 - - + -
246M ALA 3.5 2.7 - - - +
247M ARG* 4.5 12.1 - - + -
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Residues in contact with GLN 184 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115M TYR* 3.9 8.6 - - - -
182M THR* 3.1 19.8 + - - +
183M ILE* 1.3 75.8 - - - +
185M TRP* 1.3 62.0 + - - +
186M VAL* 5.0 0.4 - - + -
196M TRP* 2.6 38.2 + - + +
198M GLY 3.8 1.6 - - - -
199M TYR* 3.2 26.1 - - - +
244M TYR 3.4 1.7 - - - +
245M CYS* 3.2 3.1 - - - -
246M ALA* 2.4 56.2 + - + +
248M LYS* 3.7 23.4 - - + +
256M LEU* 3.5 33.9 - - + +
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Residues in contact with TRP 185 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155M GLN* 3.1 32.3 - - - -
169M MET* 3.7 27.1 - - + -
170M PRO 4.2 1.6 - - - -
171M CYS* 3.7 25.8 - - + -
183M ILE* 4.0 12.1 - - + +
184M GLN* 1.3 76.9 - - - +
186M VAL* 1.3 65.1 + - - +
196M TRP* 3.8 2.1 - - - -
197M ILE* 2.8 29.4 + - + +
198M GLY 2.9 19.0 + - - +
200M ILE 5.4 0.4 - - - -
219M LEU* 3.5 20.3 - - + +
228M VAL* 3.5 24.5 - - + +
230M MET* 3.5 52.3 - - + -
243M TYR* 4.5 6.7 - - + -
244M TYR 3.5 9.4 - - - -
245M CYS* 4.0 10.3 - - + -
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Residues in contact with VAL 186 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117M PHE* 4.0 23.8 - - + -
184M GLN 5.0 1.8 - - - +
185M TRP* 1.3 81.7 - - - +
187M LYS* 1.3 60.6 + - - +
188M GLN 4.2 0.2 + - - -
194M LEU* 4.7 8.3 - - + -
195M GLU 3.2 12.8 - - - +
196M TRP* 3.9 14.6 - - + -
197M ILE* 3.9 4.4 - - - +
242M VAL 3.9 0.2 - - - +
243M TYR* 3.3 6.2 - - - +
244M TYR* 2.9 50.7 + - + +
246M ALA* 5.4 0.4 - - + -
256M LEU* 4.3 13.0 - - + -
259M TRP* 3.4 27.4 - - + -
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Residues in contact with LYS 187 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186M VAL* 1.3 73.4 - - - +
188M GLN* 1.3 60.0 + - - +
189M THR* 3.7 15.6 - - + +
194M LEU* 3.4 2.5 - - - -
195M GLU* 2.7 55.4 + - - +
197M ILE* 3.7 8.7 - - + +
213M PHE* 3.8 24.2 - - + -
216M LYS* 5.1 1.6 - - - +
238M GLU* 3.3 23.0 + - - +
239M ASP* 3.9 13.6 + - - +
241M ALA* 3.6 22.7 - - + -
242M VAL 3.7 2.7 - - - -
243M TYR* 3.5 37.9 + - + +
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Residues in contact with GLN 188 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M GLN* 2.8 40.4 + - - +
106M TYR* 3.5 12.9 + - - -
187M LYS* 1.3 73.1 - - - +
189M THR* 1.3 68.6 + - - +
190M PRO* 4.6 1.2 - - - +
193M GLY* 3.4 6.7 - - - +
194M LEU* 3.5 30.6 - - + +
241M ALA* 3.2 17.5 - - - +
242M VAL* 2.9 29.9 + - + +
244M TYR* 2.7 35.4 + - + +
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Residues in contact with THR 189 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187M LYS* 3.7 21.8 - - + +
188M GLN* 1.3 82.6 - - - +
190M PRO* 1.3 68.4 - - - +
191M ARG* 3.6 10.7 - - + +
192M GLN* 2.8 35.0 + - + +
193M GLY* 2.7 36.3 + - - -
195M GLU* 4.6 4.3 - - - +
238M GLU 4.9 3.8 - - - +
240M SER 4.6 4.5 - - - +
241M ALA* 3.6 20.2 - - + -
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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