Contacts of the strand formed by residues 198 - 207 (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 GLN 198 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194M GLU* 3.4 2.1 - - - -
195M ILE 2.9 28.5 + - - +
196M ASP* 2.9 34.9 + - - +
197M GLY* 1.3 77.1 - - - +
199M LYS* 1.3 60.9 + - - +
200M LEU 3.9 0.6 + - - -
227M ASP 4.4 4.8 + - - -
228M LEU* 4.0 22.2 - - + +
229M ASN* 4.1 22.8 - - - +
233M PHE* 3.2 28.5 - - + -
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Residues in contact with LYS 199 (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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192M ASP* 5.5 0.9 - - - +
193M MET 3.3 9.6 - - - +
194M GLU* 4.0 15.3 - - + +
197M GLY 4.6 6.5 - - - +
198M GLN* 1.3 71.9 - - - +
200M LEU* 1.3 60.2 + - - +
201M ARG* 3.4 46.5 + - + +
228M LEU* 6.1 1.3 - - - -
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Residues in contact with LEU 200 (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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191M LEU* 3.2 18.9 - - + +
192M ASP* 3.1 4.5 - - - -
193M MET* 2.8 47.1 + - + +
198M GLN 3.9 2.4 + - - -
199M LYS* 1.3 69.6 - - - +
201M ARG* 1.3 60.5 + - - +
202M ASP* 4.6 11.2 - - + +
222M LEU* 4.1 9.4 - - + -
226M LEU* 3.6 31.2 - - + -
228M LEU* 4.1 11.9 - - + -
233M PHE* 4.1 18.2 - - + -
237M ILE* 3.6 36.8 - - + -
488N ARG* 4.7 1.3 - - - +
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Residues in contact with ARG 201 (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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191M LEU 3.2 5.4 - - - +
192M ASP* 3.2 36.3 + - - +
199M LYS* 3.4 44.2 + - + +
200M LEU* 1.3 72.5 - - - +
202M ASP* 1.3 61.4 + - - +
362M GLU* 4.3 8.1 + - - -
365M ILE* 2.8 36.9 - - - +
488N ARG* 4.5 7.1 + - - -
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Residues in contact with ASP 202 (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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190M ARG* 3.7 2.6 - - - +
191M LEU* 2.9 45.7 + - + +
200M LEU* 3.9 9.6 - - + -
201M ARG* 1.3 75.1 - - - +
203M ALA* 1.3 69.9 + - - +
204M PHE* 2.9 31.2 - - - +
222M LEU* 5.7 0.7 - - + -
487N ARG* 2.9 24.8 + - - +
488N ARG* 2.8 40.9 + - - +
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Residues in contact with ALA 203 (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 3.4 8.1 - - - +
190M ARG* 4.6 5.2 - - + -
202M ASP* 1.3 83.9 + - - +
204M PHE* 1.3 60.9 + - - +
309M THR* 4.6 14.0 + - - -
310M THR* 4.7 17.0 - - + +
313M TYR* 3.8 39.9 - - + +
487N ARG* 5.2 0.9 + - - -
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Residues in contact with PHE 204 (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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188M PRO* 3.7 0.2 - - - +
189M ILE* 2.9 63.4 + - + +
191M LEU* 3.8 24.2 - - + -
202M ASP* 2.9 21.5 - - - -
203M ALA* 1.3 74.8 - - - +
205M THR* 1.3 79.7 + - - +
206M TRP* 4.0 10.8 - + + -
218M PHE* 3.6 31.4 - + - -
241M ILE* 4.0 8.5 - - + -
309M THR* 5.9 3.6 - - - -
313M TYR* 3.7 10.0 - - - -
487N ARG* 3.7 13.0 - - - +
494N VAL* 3.6 34.3 - - + -
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Residues in contact with THR 205 (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* 3.3 41.7 - - + -
187M VAL 3.4 10.5 + - - +
188M PRO* 4.6 1.6 - - - +
189M ILE 4.5 0.2 - - - +
204M PHE* 1.3 82.5 + - - +
206M TRP* 1.3 62.8 + - - +
291M GLU* 4.6 4.3 + - - +
312M ALA* 5.2 1.4 - - - +
313M TYR* 4.3 13.0 + - - +
316M ARG* 4.1 20.2 - - - -
492N GLY 3.7 12.3 + - - +
493N ASP* 3.7 0.9 - - - -
494N VAL* 3.0 32.1 + - - +
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Residues in contact with TRP 206 (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* 4.2 2.7 - - - -
187M VAL* 2.9 34.8 + - + +
189M ILE* 3.7 22.4 - - + +
204M PHE* 4.0 10.3 - + + -
205M THR* 1.3 74.3 - - - +
207M ASN* 1.3 92.5 + - - +
208M MET* 3.3 5.5 + - - +
210M GLU* 4.4 5.3 + - + +
213M MET* 3.9 19.7 - - - -
214M THR 4.0 3.4 - - - -
215M PRO* 3.9 26.7 - - + -
218M PHE* 3.6 42.6 - + + -
241M ILE* 4.5 9.2 - - + -
245M ILE* 3.4 31.7 - - + +
493N ASP* 4.1 1.1 - - - -
494N VAL* 3.8 17.3 - - + -
495N CYS* 3.9 19.7 - - - -
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Residues in contact with ASN 207 (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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179M ASN* 5.4 1.2 + - - -
182M GLN 5.7 1.2 + - - -
183M PRO 4.9 0.6 + - - -
184M GLU* 3.5 19.8 - - - +
185M VAL 3.1 23.7 + - - -
186M LEU* 3.8 8.4 - - + +
206M TRP* 1.3 86.8 + - - +
208M MET* 1.3 66.7 + - - +
209M ASN* 3.2 25.7 + - - +
210M GLU* 3.3 19.9 + - + +
457N LYS* 4.1 10.1 - - - +
493N ASP* 3.1 36.7 + - + +
495N CYS* 4.6 0.2 - - - -
499N ARG* 5.6 0.4 - - - +
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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