Contacts of the strand formed by residues 193 - 201 (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 GLY 193 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106M TYR* 5.6 6.7 - - - -
119M SER* 5.7 5.6 - - - -
188M GLN* 3.4 3.7 - - - -
189M THR 2.7 36.4 + - - -
190M PRO 4.5 1.0 + - - -
191M ARG 3.6 1.6 - - - -
192M GLN* 1.3 78.7 - - - +
194M LEU* 1.3 61.8 + - - -
195M GLU* 2.8 13.5 - - - +
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Residues in contact with LEU 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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55M TYR* 6.2 1.1 - - + -
57M GLN* 4.2 3.4 - - - +
63M PRO* 5.0 5.6 - - + -
106M TYR* 3.7 42.0 - - + -
117M PHE* 3.7 51.7 + - + +
118M GLY 5.3 3.4 + - - -
186M VAL* 4.7 10.3 - - + -
187M LYS 3.4 4.5 - - - +
188M GLN* 3.5 44.0 - - + +
192M GLN 3.8 1.6 + - - +
193M GLY* 1.3 69.7 - - - -
195M GLU* 1.3 66.5 + - - +
244M TYR* 4.4 13.9 - - + -
259M TRP* 5.1 3.6 - - + -
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Residues in contact with GLU 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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117M PHE* 4.6 1.3 - - - -
186M VAL* 3.2 7.3 - - - -
187M LYS* 2.7 62.9 + - + +
189M THR* 4.4 4.4 + - - +
192M GLN* 2.7 42.4 - - - +
193M GLY 2.8 8.6 - - - +
194M LEU* 1.3 79.9 - - - +
196M TRP* 1.3 62.2 + - - +
197M ILE* 3.6 0.3 + - - +
210M ASN* 5.4 3.6 - - - +
212M LYS* 4.4 19.7 + - - +
213M PHE* 4.4 18.2 - - + -
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Residues in contact with TRP 196 (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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113M SER 3.3 24.9 - - - -
114M PRO* 4.1 5.8 - - + -
115M TYR* 3.5 57.4 + + + +
117M PHE* 4.2 13.5 - + + -
184M GLN* 2.6 28.2 + - + -
185M TRP 3.9 12.8 - - - -
186M VAL* 3.9 11.9 - - + -
195M GLU* 1.3 71.4 - - - +
197M ILE* 1.3 58.9 + - - +
198M GLY* 3.8 17.8 - - - -
199M TYR* 3.5 26.2 - + - -
208M LYS* 4.3 24.7 - - + -
209M TYR 4.4 1.3 - - - -
210M ASN* 3.0 51.8 + - + +
213M PHE* 4.2 2.3 - - - -
256M LEU* 5.6 3.1 - - + -
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Residues in contact with ILE 197 (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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185M TRP* 2.8 16.1 + - + +
186M VAL 3.9 4.9 - - - +
187M LYS* 3.7 17.9 - - + +
196M TRP* 1.3 75.1 - - - +
198M GLY* 1.3 56.0 + - - +
209M TYR* 3.5 6.8 - - + +
210M ASN* 2.7 32.7 + - - +
213M PHE* 3.6 35.9 - - + +
217M ALA* 3.7 29.4 - - + -
219M LEU* 5.8 1.6 - - + -
230M MET* 4.0 17.7 - - - -
232M LEU* 5.9 0.7 - - + -
243M TYR* 3.5 39.5 - - + -
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Residues in contact with GLY 198 (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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184M GLN* 3.8 0.3 - - - -
185M TRP* 2.9 30.4 + - - +
196M TRP* 3.8 16.6 + - - -
197M ILE* 1.3 81.9 - - - +
199M TYR* 1.3 61.5 + - - +
208M LYS 3.1 14.8 - - - -
209M TYR* 4.2 2.0 - - - -
219M LEU* 3.7 11.7 - - - +
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Residues in contact with TYR 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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115M TYR* 5.0 10.5 - + - -
182M THR* 4.4 15.3 - - + -
183M ILE 3.2 9.2 - - - +
184M GLN* 3.2 33.7 - - - +
196M TRP* 3.5 22.9 - + - -
198M GLY* 1.3 73.2 - - - -
200M ILE* 1.3 68.0 + - - +
201M TYR* 4.3 6.7 - - + -
206M GLY 4.7 6.5 - - - -
207M THR* 3.8 8.7 + - - -
208M LYS* 3.1 68.4 + - + +
219M LEU* 3.4 14.0 - - - +
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Residues in contact with ILE 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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182M THR* 3.3 3.8 - - - -
183M ILE* 3.0 37.0 + - + +
185M TRP* 5.3 0.2 - - - +
199M TYR* 1.3 76.2 - - - +
201M TYR* 1.3 62.5 + - - +
202M PRO* 3.4 6.5 - - + +
205M ALA* 4.4 9.6 - - + +
206M GLY 3.3 17.0 - - - +
207M THR* 3.5 21.3 - - + -
219M LEU* 3.8 30.2 - - + +
220M THR* 4.5 5.6 - - - -
221M SER* 4.4 17.9 - - - +
228M VAL* 3.6 38.6 - - + -
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Residues in contact with TYR 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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89C ASN 3.4 23.8 - - - -
90C ASP* 2.9 23.6 + - - -
91C GLU* 3.2 18.7 + - - +
92C GLU* 4.9 0.3 + - - +
179M THR 3.4 16.2 - - - -
180M SER 3.6 17.7 + - - -
182M THR* 3.5 27.6 - - + -
199M TYR* 4.3 7.5 - - + -
200M ILE* 1.3 73.0 - - - +
202M PRO* 1.3 62.0 - - + +
203M TYR* 3.1 18.7 + + + -
204M ASN* 3.3 21.0 + - - +
205M ALA* 2.7 34.3 + - - -
206M GLY* 3.2 16.2 + - - +
250M SER* 3.6 8.9 + - - -
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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