Contacts of the strand formed by residues 218 - 225 (chain A) in PDB entry 1X3W
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 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A CYS* 3.8 25.0 - - + -
213A TRP* 6.0 0.2 - - - -
214A ASN* 2.7 37.7 + - + +
216A GLU 3.5 1.2 - - - -
217A ASP* 1.3 83.4 + - - +
219A VAL* 1.3 70.6 + - - +
220A TRP* 3.4 24.7 - + + -
235A ASP* 3.4 20.6 + - - -
237A CYS* 4.9 4.5 - - + -
247A TYR* 3.4 25.7 - + + -
251A TRP* 4.1 13.0 - + - -
253A LYS* 3.8 17.5 - - - +
255A MSE 5.6 0.2 - - + -
2C FRU 3.8 30.6 + - - -
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Residues in contact with VAL 219 (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 CYS* 3.7 23.2 - - - +
192A GLY* 4.5 7.2 - - - -
195A CYS* 3.8 17.8 - - + +
211A TYR* 3.6 33.0 - - + +
212A VAL 3.2 15.3 - - - +
213A TRP* 3.7 21.8 - - + -
218A HIS* 1.3 95.0 + - - +
220A TRP* 1.3 68.2 + - - +
235A ASP* 4.5 3.1 - - - +
237A CYS* 5.3 1.2 - - - -
1E GLC 5.9 1.3 - - - -
2E FRU 5.8 5.2 - - - +
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Residues in contact with TRP 220 (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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195A CYS* 3.6 15.5 - - - -
211A TYR 3.8 0.2 - - - -
212A VAL* 2.8 53.7 + - + +
214A ASN* 3.7 26.5 - - + -
218A HIS* 3.4 27.6 - + + -
219A VAL* 1.3 79.0 - - - +
221A CYS* 1.3 68.1 + - - +
233A HIS* 3.3 17.4 - + - -
234A VAL 3.5 9.6 - - - +
235A ASP* 3.9 10.5 - - + +
236A SER 5.8 0.4 - - - +
247A TYR* 3.2 37.7 - + - +
255A MSE 4.3 2.5 - - + -
258A CYS* 3.7 19.7 - - - -
273A TYR* 2.9 49.4 + + - -
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Residues in contact with CYS 221 (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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195A CYS* 4.6 3.6 - - - -
198A PHE* 4.2 14.8 - - - -
199A THR* 3.7 34.3 - - - +
202A LEU* 4.3 5.6 - - - -
209A VAL* 4.1 6.5 - - + -
210A ARG 3.0 19.1 - - - +
211A TYR* 4.3 0.4 - - - -
212A VAL* 3.6 4.3 - - - -
220A TRP* 1.3 83.5 - - - +
222A GLU* 1.3 54.6 + - - +
234A VAL* 2.5 65.6 + - - +
235A ASP* 4.8 1.1 - - - +
236A SER* 5.8 2.0 - - - -
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Residues in contact with GLU 222 (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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209A VAL* 3.2 9.0 - - - +
210A ARG* 2.8 67.1 + - - -
212A VAL* 3.5 11.9 - - + +
221A CYS* 1.3 76.4 - - - +
223A TYR* 1.3 60.7 + - - +
231A TRP* 3.7 15.5 - - + -
232A VAL 3.2 13.9 - - - +
233A HIS* 4.1 2.9 - - - +
260A ALA* 4.2 2.1 - - - +
269A VAL* 3.8 7.1 - - - +
272A ARG* 2.8 29.9 + - - -
273A TYR* 2.5 35.9 + - - +
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Residues in contact with TYR 223 (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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105A THR* 3.1 23.9 + - - +
106A ASP* 2.6 30.0 + - - -
109A VAL* 3.4 36.6 - - + -
202A LEU* 4.6 14.1 - - + -
207A LEU* 4.2 19.5 - - + -
208A ASP 3.2 10.3 - - - +
209A VAL* 5.1 0.2 - - + -
222A GLU* 1.3 76.2 - - - +
224A PHE* 1.3 87.1 + - - +
225A SER* 3.6 15.4 - - - -
226A ASN 5.4 0.2 - - - -
231A TRP* 3.3 4.0 - - - -
232A VAL* 2.6 35.9 + - + +
234A VAL* 3.9 18.4 - - + -
241A PHE* 4.0 16.6 - + - -
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Residues in contact with PHE 224 (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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208A ASP* 3.0 26.4 + - + +
223A TYR* 1.3 88.6 - - - +
225A SER* 1.3 81.0 + - - +
226A ASN* 3.6 24.6 + - - +
229A ASN* 3.5 14.6 - - + -
230A ARG* 3.6 28.5 - - - -
231A TRP* 3.3 37.6 - + + -
315A ARG* 3.7 41.7 - - + -
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Residues in contact with SER 225 (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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106A ASP* 2.9 25.1 + - - -
223A TYR* 3.6 17.7 + - - -
224A PHE* 1.3 75.3 - - - +
226A ASN* 1.3 51.0 + - - +
227A PHE 3.3 4.9 + - - -
228A LEU* 3.1 34.6 + - - +
229A ASN* 2.5 37.8 + - - -
230A ARG 3.1 9.0 + - - -
232A VAL* 4.4 7.2 - - - -
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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