Contacts of the strand formed by residues 201 - 211 (chain A) in PDB entry 1XZ0
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 HIS 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A SER* 2.9 25.9 + - - -
197A PRO* 4.0 16.3 - - + +
198A GLY* 3.1 12.6 + - - +
199A PRO 3.1 22.4 + - - -
200A GLY* 1.3 81.7 + - - +
202A LEU* 1.3 72.0 + - - +
250A GLU* 5.6 2.9 - - + -
251A VAL* 3.4 8.3 - - - +
252A ALA* 3.7 29.4 - - + +
253A ALA 4.4 0.2 - - - +
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Residues in contact with LEU 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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193A HIS* 5.3 13.5 - - + +
196A SER* 4.9 3.4 - - - +
197A PRO* 3.8 9.4 - - - +
201A HIS* 1.3 81.8 - - - +
203A GLN* 1.3 62.0 + - - +
204A LEU* 4.2 20.2 - - + -
250A GLU* 3.3 5.4 - - - +
251A VAL* 2.9 31.3 + - + +
253A ALA* 3.9 28.0 - - + +
256A ALA* 4.5 15.9 - - + -
277A TRP* 4.9 11.4 - - + +
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Residues in contact with GLN 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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193A HIS* 3.7 6.9 + - - +
194A GLY* 2.9 35.8 + - - +
195A PRO* 3.2 47.4 + - - +
196A SER* 4.9 0.8 - - - +
197A PRO* 4.1 4.3 - - + +
202A LEU* 1.3 74.7 - - - +
204A LEU* 1.3 72.6 + - - +
205A VAL* 3.8 8.7 - - - +
246A ARG* 5.8 0.5 + - - -
248A THR* 3.9 19.2 + - - +
249A LEU 3.4 8.1 - - - +
250A GLU* 3.0 30.2 + - + +
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Residues in contact with LEU 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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192A SER 4.1 2.7 - - - -
193A HIS* 5.7 0.2 - - - +
202A LEU* 4.3 19.7 - - + -
203A GLN* 1.3 79.2 - - - +
205A VAL* 1.3 59.9 + - - +
220A TRP* 3.6 34.9 + - + -
247A ALA 4.0 0.5 - - - +
248A THR* 3.2 7.6 - - - -
249A LEU* 2.7 42.7 + - + +
251A VAL* 4.6 10.5 - - + -
256A ALA* 5.3 0.9 - - + -
259A LEU* 3.7 29.8 - - + -
277A TRP* 3.7 48.2 - - + +
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Residues in contact with VAL 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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191A LEU* 3.3 6.4 - - - +
192A SER* 2.9 43.8 + - - +
193A HIS 4.1 1.3 - - - +
194A GLY* 3.6 31.4 - - - +
203A GLN* 3.8 5.4 - - - +
204A LEU* 1.3 77.2 - - - +
206A CYS* 1.3 64.0 + - - +
207A HIS* 3.6 28.0 - - + +
220A TRP* 4.0 3.1 - - - -
246A ARG* 4.1 27.1 - - + +
247A ALA 3.9 2.5 - - - -
248A THR* 3.8 22.9 - - + -
277A TRP* 4.9 0.4 - - - -
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Residues in contact with CYS 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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189A ALA* 5.4 0.7 - - - -
190A TRP 3.7 4.7 - - - -
191A LEU* 4.0 8.3 - - + -
205A VAL* 1.3 76.8 - - - +
207A HIS* 1.3 66.6 + - - +
208A VAL* 4.0 5.4 + - - +
218A VAL* 4.1 9.2 - - - -
220A TRP* 3.6 13.9 - - + +
245A LEU 4.0 0.2 - - - +
246A ARG* 3.4 2.9 - - - -
247A ALA* 3.0 38.0 + - + +
261A CYS* 2.1 47.6 - - + -
263A VAL* 5.0 1.3 - - - -
275A LEU* 5.2 3.6 - - - -
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Residues in contact with HIS 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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189A ALA* 3.2 27.2 - - - +
190A TRP* 2.9 67.9 + + + -
192A SER* 3.2 24.9 + - - -
205A VAL* 3.6 19.8 - - + +
206A CYS* 1.3 72.1 - - - +
208A VAL* 1.3 60.5 + - - +
209A SER 4.3 0.2 - - - -
244A TYR* 2.8 29.1 + - + +
245A LEU 3.7 4.9 - - - +
246A ARG* 3.9 20.2 - - - +
97B ARG 4.6 8.2 + - - -
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Residues in contact with VAL 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* 3.7 26.7 - - + -
188A GLU 3.6 4.9 - - - +
189A ALA* 4.8 2.5 - - + -
206A CYS* 4.7 4.9 - - - +
207A HIS* 1.3 76.8 - - - +
209A SER* 1.3 65.5 + - - +
211A PHE* 3.5 17.7 - - + -
216A VAL* 4.7 5.2 - - + -
218A VAL* 3.9 22.4 - - + -
244A TYR* 3.5 2.1 - - - -
245A LEU* 2.8 47.1 + - + +
263A VAL* 3.8 35.0 - - + -
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Residues in contact with SER 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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187A PRO* 3.3 2.9 - - - +
188A GLU* 3.0 38.7 + - - +
190A TRP* 3.7 12.2 - - - -
208A VAL* 1.3 77.1 - - - +
210A GLY* 1.3 60.9 + - - +
211A PHE* 3.5 4.0 - - - -
243A TRP 3.5 6.3 - - - -
244A TYR* 3.4 27.8 - - - -
12B ARG* 2.9 32.2 + - - -
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Residues in contact with GLY 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 VAL* 3.4 27.4 - - - +
186A LYS 4.0 4.3 - - - +
187A PRO* 4.3 3.6 - - - -
209A SER* 1.3 75.7 + - - +
211A PHE* 1.3 55.9 + - - -
238A SER* 5.8 0.4 + - - -
242A THR* 3.5 24.8 - - - +
243A TRP 2.9 10.7 + - - -
12B ARG* 3.8 19.0 + - - +
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Residues in contact with PHE 211 (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 VAL 3.4 7.0 - - - +
187A PRO* 3.9 12.8 - - + -
208A VAL* 3.5 42.0 - - + -
209A SER* 4.2 4.0 - - - -
210A GLY* 1.3 78.0 - - - +
212A TYR* 1.3 63.9 + - - +
213A PRO 3.6 13.0 - - - -
214A LYS 3.5 20.4 - - - -
216A VAL* 3.8 19.7 - - + -
235A ILE* 4.5 6.7 - - + -
242A THR* 3.7 0.6 - - - -
243A TRP* 3.1 66.2 + + + -
244A TYR* 4.0 3.4 - - - -
245A LEU* 4.2 10.8 - - + -
265A HIS* 3.7 24.0 - + + +
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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