Contacts of the strand formed by residues 193 - 201 (chain N) 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 GLY 193 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106N TYR* 5.0 13.5 - - - -
118N GLY 5.7 1.6 - - - -
119N SER* 5.6 4.7 - - - -
187N LYS 3.5 1.4 - - - +
188N GLN* 3.5 3.7 - - - -
189N THR* 3.1 37.1 + - - +
190N PRO 4.8 0.2 - - - -
191N ARG 3.4 3.6 + - - +
192N GLN* 1.3 82.4 - - - +
194N LEU* 1.3 62.7 + - - -
195N GLU* 4.9 1.2 - - - +
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Residues in contact with LEU 194 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55N TYR* 6.0 1.1 - - + -
57N GLN* 4.0 5.4 - - - +
63N PRO* 4.7 11.0 - - + -
106N TYR* 3.5 47.5 - - + -
117N PHE* 3.7 49.1 + - + +
118N GLY 5.2 1.8 + - - +
186N VAL* 3.6 22.0 - - + -
187N LYS 3.5 1.8 - - - -
188N GLN* 3.2 33.7 - - + +
192N GLN 4.1 4.5 - - - +
193N GLY* 1.3 73.4 - - - -
195N GLU* 1.3 62.5 + - - +
244N TYR* 4.4 7.4 - - + -
259N TRP* 4.8 2.0 - - + -
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Residues in contact with GLU 195 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20N ASP* 5.4 4.7 - - - +
115N TYR 3.9 11.1 - - - +
116N THR* 5.1 4.5 - - - +
117N PHE* 4.5 3.4 + - - -
186N VAL* 3.2 7.2 - - - +
187N LYS* 2.6 55.2 + - + +
189N THR* 6.4 0.9 - - + -
192N GLN* 5.5 6.5 - - + +
193N GLY 4.9 1.8 - - - +
194N LEU* 1.3 78.9 - - - +
196N TRP* 1.3 76.6 + - - +
197N ILE 3.7 0.2 + - - -
210N ASN* 3.7 16.3 + - - -
212N LYS* 3.2 26.6 + - - +
213N PHE* 3.7 27.8 - - + -
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Residues in contact with TRP 196 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113N SER 3.2 25.8 - - - -
114N PRO* 3.8 7.2 - - + -
115N TYR* 3.4 52.2 - + + +
117N PHE* 4.2 13.4 - + + -
184N GLN* 2.8 26.6 + - + -
185N TRP 3.9 13.0 - - - -
186N VAL* 4.5 10.5 - - + +
195N GLU* 1.3 81.0 + - - +
197N ILE* 1.3 57.9 + - - +
198N GLY* 3.5 27.3 + - - -
199N TYR* 3.6 22.7 - + - -
208N LYS* 4.3 20.9 - - + -
209N TYR 4.5 1.1 - - - -
210N ASN* 2.8 54.0 + - + +
213N PHE* 4.3 0.2 - - - -
256N LEU* 5.2 2.5 - - + -
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Residues in contact with ILE 197 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185N TRP* 2.9 16.7 + - + +
186N VAL 4.4 2.7 - - - -
187N LYS* 3.7 17.3 - - + +
196N TRP* 1.3 75.2 - - - +
198N GLY* 1.3 62.0 + - - +
209N TYR* 3.6 5.8 - - + +
210N ASN* 2.7 29.7 + - - +
213N PHE* 3.9 33.6 - - + +
217N ALA* 3.7 28.3 - - + -
219N LEU* 5.9 1.8 - - + -
230N MET* 3.9 19.5 - - + -
232N LEU* 5.3 1.8 - - + -
243N TYR* 3.5 38.6 - - + -
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Residues in contact with GLY 198 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184N GLN* 3.6 0.9 - - - -
185N TRP* 2.9 29.8 + - - +
196N TRP* 3.5 18.7 + - - -
197N ILE* 1.3 84.5 - - - +
199N TYR* 1.3 60.8 + - - +
208N LYS 3.1 14.4 - - - -
209N TYR* 4.4 1.3 - - - -
219N LEU* 4.1 8.1 - - - -
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Residues in contact with TYR 199 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115N TYR* 4.6 12.8 - + - -
182N THR* 4.1 17.0 - - + -
183N ILE 3.1 13.0 - - - +
184N GLN* 3.2 29.8 - - - +
196N TRP* 3.6 18.6 - + - -
198N GLY* 1.3 73.2 - - - -
200N ILE* 1.3 69.3 + - - +
201N TYR* 4.6 5.8 - - + -
206N GLY 4.6 6.1 - - - -
207N THR* 3.4 6.9 - - - -
208N LYS* 3.2 68.9 + - + +
219N LEU* 3.4 11.6 - - - +
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Residues in contact with ILE 200 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182N THR* 3.3 3.6 - - - -
183N ILE* 3.1 33.1 + - + +
185N TRP* 5.5 0.2 - - - +
199N TYR* 1.3 78.5 - - - +
201N TYR* 1.3 67.5 + - - +
202N PRO* 3.3 7.5 - - + +
205N ALA* 4.5 12.3 - - + +
206N GLY 3.3 4.5 - - - +
207N THR* 3.5 16.6 - - + -
219N LEU* 3.8 32.5 - - + +
220N THR* 3.8 20.4 - - - -
221N SER* 3.9 13.9 - - - +
228N VAL* 3.4 27.6 - - + -
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Residues in contact with TYR 201 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G ASN 3.3 20.4 - - - -
90G ASP* 3.1 8.6 + - - -
91G GLU* 2.5 37.7 + - + +
179N THR 4.4 3.6 - - - -
180N SER 4.0 12.6 - - - -
181N TYR 4.6 0.7 - - - -
182N THR* 3.3 26.7 - - + -
199N TYR* 4.3 6.9 - - + -
200N ILE* 1.3 72.5 - - - +
202N PRO* 1.3 55.6 - - + +
203N TYR* 3.0 26.7 + + + -
204N ASN* 3.0 23.2 + - - +
205N ALA* 2.7 33.2 + - - -
206N GLY* 2.7 18.7 + - - +
250N SER* 3.7 21.2 + - - -
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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