Contacts of the strand formed by residues 214 - 218 (chain N) in PDB entry 2X1W
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 TYR 214 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134N GLY* 3.4 25.1 - - - +
135N VAL 3.8 8.1 - - - -
136N VAL* 3.5 25.8 - - + -
148N ILE* 3.6 24.0 - - + -
149N PRO* 2.9 45.5 + - + +
150N CYS* 3.9 13.3 + - - -
197N MET* 3.2 8.2 - - - +
198N VAL* 2.8 45.5 + - + +
199N PHE* 4.6 0.9 - - - -
211N SER* 4.0 2.1 - - - -
212N ILE* 3.0 48.1 - - + +
213N MET* 1.3 73.4 - - - +
215N ILE* 1.3 62.1 + - - +
216N VAL 3.6 0.5 + - - -
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Residues in contact with ILE 215 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 6.4 2.0 - - + -
126A TRP* 4.7 11.7 - - + -
153B LYS* 4.6 17.9 - - + -
186B PHE* 3.4 39.3 - - + -
196B PRO* 4.6 10.1 - - + -
133N HIS* 3.7 26.9 - - + +
134N GLY 2.7 17.9 + - - +
135N VAL* 3.3 10.2 - - + +
136N VAL 2.8 25.9 + - - -
196N GLY 4.0 7.2 - - - +
197N MET* 4.6 4.0 - - + -
213N MET* 5.6 1.8 - - + +
214N TYR* 1.3 70.8 - - - +
216N VAL* 1.3 73.1 + - - +
217N VAL* 4.0 10.8 - - + -
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Residues in contact with VAL 216 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A TRP* 5.8 0.2 - - - -
167A ASN* 6.2 0.3 - - - +
153B LYS* 3.9 14.4 + - - +
136N VAL* 3.7 8.3 - - + +
138N ILE* 3.6 32.3 - - + -
192N ILE* 4.0 8.3 - - + +
193N SER* 4.8 1.1 - - - +
195N ALA 3.3 25.5 - - - +
196N GLY* 3.0 18.0 + - - +
197N MET* 3.9 12.8 - - - -
198N VAL* 3.9 26.5 - - + +
214N TYR 4.2 0.7 - - - +
215N ILE* 1.3 73.9 - - - +
217N VAL* 1.3 72.6 + - - +
218N VAL* 4.2 6.9 + - + +
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Residues in contact with VAL 217 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B PHE* 6.2 2.5 - - + -
153B LYS* 4.5 5.6 - - - +
188B ILE* 3.4 37.9 - - + -
196B PRO* 5.0 0.7 - - + -
135N VAL* 3.6 24.7 - - + -
136N VAL 2.9 8.4 + - - +
137N TYR* 3.5 26.8 - - + -
138N ILE 3.0 22.4 + - - -
215N ILE* 3.9 8.7 - - + +
216N VAL* 1.3 81.2 - - - +
218N VAL* 1.3 60.9 + - - +
219N VAL* 3.2 24.4 + - + +
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Residues in contact with VAL 218 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ASN* 5.2 4.3 - - + +
168A SER* 3.5 21.3 - - - +
151B PHE* 4.8 5.5 - - - -
153B LYS* 4.8 7.2 + - - +
138N ILE* 3.7 17.0 - - + +
140N GLU* 3.9 29.2 - - + +
193N SER* 3.7 32.5 - - - +
216N VAL* 4.2 4.6 + - + -
217N VAL* 1.3 72.1 - - - +
219N VAL* 1.3 60.7 + - - +
253N ASN* 3.2 40.1 - - + +
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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