Contacts of the strand formed by residues 193 - 202 (chain A) in PDB entry 1PCU
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 LYS 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A LEU* 3.6 1.7 - - - -
189A ASP* 3.1 45.9 + - - +
191A LYS* 3.5 18.0 + - - -
192A LYS* 1.3 76.1 - - - +
194A LEU* 1.3 86.3 + - + +
195A ALA* 3.5 6.1 + - + +
215A GLU* 5.4 1.6 - - - +
217A LYS* 4.6 8.5 - - - +
303A HIS* 3.6 20.8 + - - +
306A ARG* 5.8 2.0 - - - +
307A GLU* 4.4 25.2 - - - +
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Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A VAL* 3.8 22.4 - - + -
187A LEU 4.0 5.2 - - - -
188A LEU* 3.7 22.9 - - + -
192A LYS 4.2 6.3 - - - +
193A LYS* 1.3 95.3 - - + +
195A ALA* 1.3 58.8 + - - +
228A LEU* 4.1 35.4 - - + -
300A TRP* 4.6 12.1 - - + -
302A TYR* 5.8 1.3 - - + -
303A HIS* 3.1 44.3 - - + +
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Residues in contact with ALA 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A VAL* 5.6 0.4 - - - +
187A LEU* 3.0 18.6 + - + +
193A LYS* 3.5 5.6 + - + +
194A LEU* 1.3 73.5 - - - +
196A CYS* 1.3 74.1 + - + +
215A GLU* 4.0 33.9 - - + +
219A LEU* 4.4 6.1 - - + -
303A HIS* 4.1 1.9 - - - -
357A GLU* 5.6 0.9 - - - +
358A GLY* 3.7 20.8 + - - -
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Residues in contact with CYS 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A VAL* 4.0 5.0 - - - +
187A LEU* 3.0 45.4 + - + +
195A ALA* 1.3 89.9 - - + +
197A GLY* 1.3 60.4 + - - +
208A THR* 4.0 2.5 - - - +
212A CYS* 2.0 50.0 - - + -
215A GLU* 6.4 0.2 - - - -
300A TRP* 5.9 0.2 - - - -
358A GLY 3.4 11.9 - - - +
360A SER* 3.4 11.4 - - - +
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Residues in contact with GLY 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A GLN* 4.3 6.7 - - - -
185A VAL 3.8 5.8 - - - -
186A VAL* 5.2 0.7 - - - -
187A LEU* 4.0 0.2 - - - +
196A CYS* 1.3 72.9 - - - +
198A ALA* 1.3 59.5 + - - +
208A THR* 2.7 28.4 + - - -
300A TRP* 5.6 3.8 - - - -
358A GLY 3.1 10.7 + - - -
359A ASP* 4.4 3.1 - - - -
360A SER 2.9 11.7 + - - -
361A GLY 3.2 18.4 - - - +
362A GLY* 4.1 3.4 - - - -
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Residues in contact with ALA 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A TRP 3.5 1.0 - - - +
184A GLN* 3.3 9.3 + - - +
185A VAL* 3.0 43.5 + - + +
187A LEU* 3.8 25.6 - - + -
197A GLY* 1.3 74.7 - - - +
199A VAL* 1.3 65.7 + - - +
206A VAL* 3.8 16.2 - - + -
207A LEU 3.2 14.4 - - - +
208A THR* 4.5 0.2 - - - -
261A LEU* 4.8 0.2 - - + -
361A GLY 3.8 2.8 + - - -
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Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A TRP* 3.4 11.0 - - + -
185A VAL* 4.9 0.2 - - - -
198A ALA* 1.3 81.0 - - - +
200A LEU* 1.3 64.6 + - - +
201A ILE 3.4 1.4 + - - -
206A VAL* 3.4 5.7 - - - +
207A LEU* 2.8 40.6 + - + +
276A ILE* 3.8 42.8 - - + -
361A GLY 3.7 7.6 - - - +
363A PRO* 3.7 31.4 - - + -
374A LEU* 4.8 1.1 - - + -
377A LEU* 3.7 24.7 - - + -
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A TRP* 3.3 14.1 + - + +
185A VAL* 4.8 0.8 - - - +
199A VAL* 1.3 70.7 - - - +
201A ILE* 1.3 58.7 + - - +
202A HIS 3.4 23.6 - - - +
203A PRO* 4.0 13.5 - - + +
205A TRP 4.2 1.8 - - - -
206A VAL* 4.1 17.9 - - + +
223A LEU* 3.7 39.9 - - + -
267A ALA* 4.1 6.1 - - + -
269A LEU* 5.3 3.6 - - + -
273A ILE* 4.2 13.9 - - + -
274A VAL 4.2 21.8 - - - +
275A PRO* 3.4 15.1 - - + +
276A ILE* 3.0 29.0 + - - +
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Residues in contact with ILE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LYS* 3.3 15.5 - - - +
199A VAL 3.4 1.8 + - - -
200A LEU* 1.3 71.3 - - - +
202A HIS* 1.3 64.5 + - + +
205A TRP* 3.2 23.8 + - + +
207A LEU* 3.7 21.1 - - + -
260A LEU* 3.7 20.6 - - + -
275A PRO* 3.2 16.4 - - - +
276A ILE* 3.7 30.4 - - + +
278A LEU* 3.8 27.8 - - + -
403A ILE* 3.9 14.1 - - + -
407A ILE* 3.7 31.4 - - + -
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Residues in contact with HIS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A HIS* 6.0 0.7 - + - -
135A PRO* 3.5 14.7 + - - +
136A ALA 3.1 25.1 - - - +
137A VAL* 3.8 18.5 - - + +
138A LYS* 4.2 8.5 - - + +
200A LEU* 3.4 10.7 - - - +
201A ILE* 1.3 81.2 - - + +
203A PRO* 1.4 75.3 - - + +
204A SER* 3.9 11.1 + - - -
205A TRP* 3.0 47.4 + + - +
275A PRO* 4.6 4.0 - - - -
407A ILE* 3.7 28.9 - - + +
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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