Contacts of the strand formed by residues 236 - 243 (chain B) in PDB entry 1XSK
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 236 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B ARG* 3.6 40.3 + - + +
69B ILE 3.3 11.2 - - - +
70B GLU* 4.0 17.3 - - + -
72B PHE 5.6 1.6 - - - +
77B ASN* 3.4 39.2 - - + +
81B HIS* 4.9 14.4 + - - -
150B MET* 3.5 7.2 - - - +
211B ASN* 4.9 4.4 + - - -
212B HIS* 3.3 32.5 + + - -
214B GLN* 6.4 0.2 - - - -
232B VAL* 4.3 0.5 - - - +
234B SER* 2.9 35.2 + - - -
235B GLU* 1.3 84.8 - - + +
237B LEU* 1.3 68.3 + - - +
238B GLU* 4.2 7.6 - - + -
435B LYS* 5.2 7.5 - - - -
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Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B VAL 3.7 0.7 - - - +
68B ARG* 3.3 2.6 - - - +
69B ILE* 2.8 50.8 + - + +
150B MET* 3.6 16.5 - - + +
151B PHE* 3.8 21.3 - - - +
152B GLU* 3.7 29.8 - - + -
210B VAL* 4.1 15.7 - - + -
212B HIS* 3.4 18.2 - - + +
230B PHE* 3.7 16.8 - - + +
232B VAL* 4.1 9.4 - - + -
236B TYR* 1.3 75.3 - - - +
238B GLU* 1.3 71.8 + - - +
239B TYR* 4.2 9.2 - - + -
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Residues in contact with GLU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PHE* 3.7 18.3 - - + -
67B VAL 3.2 10.1 - - - +
68B ARG* 2.9 38.8 + - + +
86B ILE* 6.2 0.2 - - - +
210B VAL* 3.8 1.4 - - - -
211B ASN* 2.9 54.1 + - + +
212B HIS* 3.1 14.0 + - + -
236B TYR* 4.2 13.5 - - + -
237B LEU* 1.3 78.1 - - - +
239B TYR* 1.3 64.7 + - - +
240B PHE* 3.3 19.2 - - + -
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Residues in contact with TYR 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B VAL 3.9 0.2 - - - +
66B GLY* 3.7 1.2 - - - -
67B VAL* 2.9 54.5 + - + +
69B ILE* 5.2 4.9 - - + -
120B LEU* 3.7 16.8 - - - +
122B PHE* 4.0 20.4 - + - -
152B GLU* 2.5 41.3 + - + -
154B LEU* 3.9 20.7 - - + +
208B VAL* 5.0 4.3 - - + -
209B LEU 3.2 13.2 - - - +
210B VAL* 4.2 8.1 - - + -
211B ASN 4.3 0.4 - - - +
230B PHE* 3.9 26.2 - + + -
237B LEU* 4.2 11.2 - - + -
238B GLU* 1.3 77.1 - - - +
240B PHE* 1.3 67.7 + - - +
241B VAL* 4.1 10.5 - - + -
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Residues in contact with PHE 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B PHE* 3.7 28.7 - + - -
60B PRO* 4.0 14.1 - - + -
64B ILE* 3.9 24.9 - - + -
65B VAL 3.4 2.2 - - - -
66B GLY* 3.4 15.3 - - - -
84B LEU* 4.2 5.2 - - + -
86B ILE* 5.6 4.5 - - + -
208B VAL* 3.0 8.6 - - - -
209B LEU* 3.0 43.0 + - + +
211B ASN* 3.5 32.1 - - + -
238B GLU* 3.3 22.2 - - + -
239B TYR* 1.3 75.7 - - - +
241B VAL* 1.3 62.1 + - - +
242B ILE* 3.8 5.5 + - + +
257B PHE* 3.8 26.9 - + + -
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Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ILE* 3.5 2.6 - - - -
65B VAL 3.0 31.3 + - - +
108B LEU* 3.4 25.5 - - + +
122B PHE* 3.3 53.2 - - + -
129B ILE* 4.9 3.8 - - + -
130B THR* 4.9 2.9 - - + -
154B LEU* 4.8 7.9 - - + -
206B TYR* 4.5 16.4 - - + -
207B GLY 3.5 7.4 - - - +
208B VAL* 4.5 2.7 - - + -
239B TYR* 4.1 13.9 - - + -
240B PHE* 1.3 74.1 - - - +
242B ILE* 1.3 64.0 + - - +
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Residues in contact with ILE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B GLY 3.9 2.0 - - - -
64B ILE* 3.7 24.7 - - + -
199B PHE* 3.9 26.2 - - + -
206B TYR* 3.1 8.9 - - - +
207B GLY 2.6 45.1 + - - +
209B LEU* 4.8 4.9 - - + -
240B PHE* 3.9 11.7 - - + +
241B VAL* 1.3 79.6 - - - +
243B ASP* 1.3 64.9 + - - +
250B VAL* 4.1 11.5 - - + +
253B ARG* 3.5 32.1 - - + -
254B TYR* 4.0 22.2 - - + -
257B PHE* 4.7 6.1 - - + -
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Residues in contact with ASP 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B GLY* 3.1 22.0 + - - +
107B ASN* 4.2 17.2 + - - +
108B LEU* 3.9 22.0 + - + +
124B ARG* 2.6 53.3 + - - +
129B ILE* 4.9 0.7 - - - +
205B GLY 4.3 0.9 - - - -
206B TYR* 4.6 3.8 - - - -
241B VAL 4.1 0.8 + - - -
242B ILE* 1.3 75.8 - - - +
244B GLY* 1.3 66.6 + - - +
245B PRO* 4.5 2.3 - - - +
250B VAL* 4.0 8.0 - - - -
253B ARG* 2.9 33.7 + - - +
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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