Contacts of the strand formed by residues 186 - 195 (chain M) in PDB entry 6LTJ
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 LEU 186 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184M GLU* 3.4 44.6 + - + +
185M VAL* 1.3 72.3 - - - +
187M VAL* 1.3 59.0 - - - +
188M PRO* 4.4 0.9 - - - +
205M THR* 3.3 19.5 - - + -
206M TRP 3.5 1.6 - - - -
207M ASN* 3.8 12.8 - - - +
248M TYR* 3.7 17.2 + - - -
291M GLU* 3.8 15.7 - - - +
316M ARG* 3.5 45.2 + - - +
456N SER* 5.7 2.0 - - - -
492N GLY* 4.7 0.9 - - - -
493N ASP* 3.6 28.0 - - + +
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Residues in contact with VAL 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 LEU* 1.3 76.6 - - - +
188M PRO* 1.3 68.5 - - + +
189M ILE* 3.6 26.0 - - + -
205M THR* 3.4 5.7 - - - +
206M TRP* 2.9 41.0 + - + +
208M MET* 3.7 26.0 - - + -
244M GLN 5.0 1.6 - - - +
245M ILE* 4.2 18.6 - - + +
248M TYR* 3.5 39.9 - - + -
316M ARG* 5.5 0.2 - - - -
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Residues in contact with PRO 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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186M LEU 4.4 2.0 - - - +
187M VAL* 1.3 87.2 - - + +
189M ILE* 1.3 66.5 + - - +
204M PHE 3.7 5.2 - - - +
205M THR* 4.5 3.4 - - - +
244M GLN* 3.8 11.3 - - - +
248M TYR* 3.9 17.9 - - + -
313M TYR* 3.5 29.2 - - + +
316M ARG* 4.2 21.1 - - + +
317M GLY* 4.0 22.0 - - - +
320M SER* 4.5 6.3 - - - +
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Residues in contact with ILE 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 VAL* 3.6 20.6 - - + +
188M PRO* 1.3 81.9 - - - +
190M ARG* 1.3 62.8 - - - +
191M LEU* 4.2 5.4 - - + -
203M ALA* 3.4 3.0 - - - -
204M PHE* 2.9 64.0 + - + +
206M TRP* 3.7 26.7 - - + +
241M ILE* 4.0 28.3 - - + +
244M GLN* 3.7 33.7 - - + +
245M ILE* 4.3 3.6 - - + -
313M TYR* 3.6 4.8 - - - -
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Residues in contact with ARG 190 (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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189M ILE* 1.3 75.7 - - - +
191M LEU* 1.3 70.8 + - - +
192M ASP* 4.4 11.1 + - + +
202M ASP 3.7 9.9 - - - +
203M ALA* 4.6 3.1 - - + -
240M ALA* 5.3 0.3 - - - +
244M GLN* 2.6 32.1 + - - +
313M TYR* 2.6 55.0 + - + +
368M GLN* 2.7 37.2 + - - +
369M ASP* 4.3 10.3 - - - +
372M THR* 3.1 27.2 + - - +
376M ARG* 2.6 35.4 + - - +
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Residues in contact with LEU 191 (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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189M ILE* 4.2 11.4 - - + -
190M ARG* 1.3 85.0 - - - +
192M ASP* 1.3 61.8 + - - +
193M MET* 3.6 24.2 - - + -
200M LEU* 3.2 22.0 - - + +
201M ARG* 3.2 2.4 - - - -
202M ASP* 2.9 43.4 + - + +
204M PHE* 3.8 27.8 - - + -
218M PHE* 5.1 0.2 - - + -
222M LEU* 4.3 8.3 - - + -
237M ILE* 3.8 25.8 - - + -
240M ALA* 3.9 19.3 - - + -
241M ILE* 4.6 2.7 - - + -
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Residues in contact with ASP 192 (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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71G ARG* 5.8 2.1 + - - -
190M ARG* 4.3 13.1 + - - +
191M LEU* 1.3 74.1 - - - +
193M MET* 1.3 67.1 + - - +
194M GLU* 3.7 3.6 + - - +
199M LYS* 5.5 0.9 - - - +
200M LEU 3.1 3.8 - - - -
201M ARG* 3.2 36.6 + - - +
369M ASP* 4.7 16.2 - - + +
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Residues in contact with MET 193 (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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71G ARG* 5.2 21.1 - - + +
72G ASP* 5.3 0.4 - - - -
191M LEU* 3.6 44.4 - - + -
192M ASP* 1.3 81.5 - - - +
194M GLU* 1.3 59.8 + - - +
195M ILE* 4.2 9.9 - - + -
198M GLN 4.5 0.2 - - - -
199M LYS* 3.3 4.2 - - - +
200M LEU* 2.8 36.7 + - + +
233M PHE* 4.5 17.3 - - + -
236M ALA* 3.7 31.6 - - + +
237M ILE* 3.7 29.2 - - + -
240M ALA* 4.5 5.4 - - + -
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Residues in contact with GLU 194 (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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72G ASP* 2.5 57.8 + - - +
192M ASP* 3.7 4.4 + - - +
193M MET* 1.3 75.2 - - - +
195M ILE* 1.3 60.4 + - - +
196M ASP 4.6 1.7 + - - -
197M GLY* 3.3 31.5 + - - +
198M GLN 3.4 4.0 - - - +
199M LYS* 4.0 21.5 - - + -
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Residues in contact with ILE 195 (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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71G ARG* 3.4 26.5 - - + +
72G ASP* 3.5 15.5 - - - +
74G LYS* 2.5 41.3 - - - +
193M MET* 4.6 10.3 - - + -
194M GLU* 1.3 87.6 - - - +
196M ASP* 1.3 93.2 + - + +
197M GLY 3.1 2.0 - - - -
198M GLN* 2.9 25.0 + - - +
232M THR* 3.5 3.4 - - + -
233M PHE* 3.9 24.0 - - + -
236M ALA* 5.8 7.0 - - + -
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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