Contacts of the strand formed by residues 201 - 210 (chain A) in PDB entry 3ES6
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 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A SER* 4.4 8.1 + - - -
194A HIS 3.5 16.8 - - - +
195A GLN* 3.3 37.4 + - - +
199A GLU 3.7 0.8 + - - -
200A LYS* 1.3 75.3 - - - +
202A LYS* 1.3 61.2 + - - +
203A LEU* 4.2 5.4 - - + -
249A ALA* 3.5 3.8 - - - -
250A VAL* 2.8 52.3 + - + +
252A PRO* 6.2 0.6 - - - +
275A TRP* 3.7 37.3 - - + -
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Residues in contact with LYS 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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192A THR 3.8 1.0 - - - +
193A SER* 3.5 2.4 - - - -
194A HIS* 3.0 44.2 + - + +
199A GLU* 3.8 34.7 + - + -
200A LYS* 4.0 5.2 - - - +
201A LYS* 1.3 80.2 - - - +
203A LEU* 1.3 64.3 + - - +
204A LYS* 4.0 1.3 + - - +
229A GLU* 2.7 37.7 + - - +
247A VAL* 3.9 17.5 - - + -
248A VAL 3.4 8.3 - - - +
249A ALA* 4.2 10.5 - - + -
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Residues in contact with LEU 203 (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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192A THR 3.6 2.2 - - - +
193A SER* 3.7 15.5 - - - +
201A LYS* 4.2 4.7 - - + -
202A LYS* 1.3 73.9 - - - +
204A LYS* 1.3 60.1 + - - +
219A TRP* 3.4 25.5 + - + -
247A VAL* 3.3 4.4 - - - -
248A VAL* 2.9 39.5 + - + +
250A VAL* 4.0 12.8 - - + -
258A TYR* 3.8 33.4 - - + -
275A TRP* 3.5 60.1 - - + +
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Residues in contact with LYS 204 (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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190A VAL 3.8 1.4 - - - +
191A VAL* 3.5 3.6 - - - -
192A THR* 2.8 47.2 + - + +
202A LYS 4.0 1.3 + - - +
203A LEU* 1.3 72.0 - - - +
205A CYS* 1.3 63.2 + - - +
206A LEU* 4.8 1.1 - - + +
219A TRP* 3.8 3.1 - - - -
245A TRP* 3.5 38.1 - - + +
246A VAL 3.5 3.4 - - - -
247A VAL* 4.0 21.8 - - + +
4C MAN 2.9 35.8 + - - +
5C NDG 3.0 25.2 + - - +
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Residues in contact with CYS 205 (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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189A VAL* 5.0 6.7 - - - -
190A VAL 3.7 3.8 - - - -
191A VAL* 4.4 8.3 - - - +
204A LYS* 1.3 71.3 - - - +
206A LEU* 1.3 65.5 + - - +
207A ALA 3.9 0.2 + - - -
217A VAL* 4.2 10.3 - - + +
219A TRP* 3.5 22.6 - - + +
244A SER 3.9 0.7 - - - +
245A TRP* 3.1 5.2 - - - -
246A VAL 2.8 33.4 + - - +
260A CYS* 2.0 50.0 - - - -
262A VAL* 4.8 5.6 - - - -
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Residues in contact with LEU 206 (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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188A SER 3.8 0.5 - - - +
189A VAL* 3.2 7.3 - - - +
190A VAL* 2.9 42.6 + - + +
204A LYS* 4.0 3.3 - - + -
205A CYS* 1.3 74.1 - - - +
207A ALA* 1.3 75.5 + - - +
208A TYR* 3.9 24.6 - - + -
243A GLN* 3.8 20.0 - - + +
244A SER 4.1 0.9 - - - +
245A TRP* 3.7 28.7 - - + -
3C BMA 4.0 2.2 - - - +
4C MAN 3.3 49.1 - - - +
5C NDG 5.2 5.4 - - + -
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Residues in contact with ALA 207 (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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187A PRO* 4.3 2.9 - - + -
188A SER 3.7 4.5 - - - -
189A VAL* 4.3 14.4 - - + -
205A CYS 3.9 0.6 + - - -
206A LEU* 1.3 73.9 - - - +
208A TYR* 1.3 63.8 + - - +
210A PHE* 3.7 15.5 - - + -
215A ILE* 4.2 7.2 - - + -
217A VAL* 4.1 22.4 - - + -
243A GLN* 3.4 2.8 - - - +
244A SER 2.7 42.8 + - - +
262A VAL* 4.6 1.1 - - + -
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Residues in contact with TYR 208 (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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187A PRO* 3.4 2.8 - - - +
188A SER* 3.0 68.9 + - - -
190A VAL* 3.7 26.1 - - + +
206A LEU* 3.9 21.5 - - + -
207A ALA* 1.3 74.2 - - - +
209A ASP* 1.3 98.1 + - - +
210A PHE* 3.3 5.2 - - - -
242A TYR 3.7 6.5 - - - -
243A GLN* 3.3 25.8 - - + +
2C NAG 3.5 24.0 - - - -
3C BMA 3.5 33.4 + - - -
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Residues in contact with ASP 209 (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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185A ASP* 3.8 11.6 - - - +
186A PRO 3.6 11.5 - - - +
188A SER* 4.8 6.2 + - - +
208A TYR* 1.3 94.0 - - + +
210A PHE* 1.3 58.4 + - - +
241A THR* 4.2 16.7 + - - +
242A TYR 3.2 7.9 + - - -
243A GLN* 4.3 3.7 + - - +
1C NAG 2.7 48.6 + - + +
2C NAG 2.8 22.1 + - - -
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Residues in contact with PHE 210 (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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185A ASP* 3.5 15.5 - - - +
187A PRO* 3.7 33.0 - - + -
207A ALA* 3.5 26.0 - - + -
208A TYR 3.8 6.1 - - - -
209A ASP* 1.3 78.3 - - - +
211A TYR* 1.3 62.4 + - - +
212A PRO 3.4 18.2 - - - -
213A GLY 3.8 11.4 - - - -
215A ILE* 3.7 38.8 - - + -
241A THR* 3.6 2.2 - - - -
242A TYR* 2.7 69.1 + + + +
243A GLN* 3.7 1.3 - - - -
244A SER* 3.8 13.0 - - - -
264A HIS* 3.9 4.5 - + - +
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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