Contacts of the strand formed by residues 230 - 237 (chain A) in PDB entry 2HTE
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 CYS 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A SER* 3.3 28.6 + - - -
195A LEU* 4.6 4.0 - - - -
196A TRP* 3.8 23.8 - - - -
220A ASN* 3.6 27.4 - - - +
221A ILE 3.1 18.6 - - - +
222A SER* 4.5 1.8 - - - -
223A ILE 3.7 3.5 + - - +
226A TYR* 3.9 7.8 + - - +
227A PRO 3.4 14.1 + - - +
228A CYS 3.2 5.3 - - - -
229A GLY* 1.3 81.8 - - - +
231A ILE* 1.3 63.8 + - - +
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Residues in contact with ILE 231 (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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64A TYR* 3.7 29.8 - - + -
191A GLN* 3.6 32.5 - - + +
193A GLU* 3.6 31.0 - - - +
194A SER* 4.5 0.9 - - - +
220A ASN* 3.7 4.9 - - - -
221A ILE* 2.9 39.1 + - + +
223A ILE* 3.9 17.5 - - + -
226A TYR* 3.7 25.1 - - + -
227A PRO* 6.2 0.7 - - + -
230A CYS* 1.3 77.1 - - - +
232A GLY* 1.3 62.2 + - - +
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Residues in contact with GLY 232 (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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68A MET* 5.2 1.4 - - - +
191A GLN* 3.7 5.2 - - - +
192A CYS* 2.8 29.2 + - - -
193A GLU 2.8 15.1 + - - -
218A TYR* 3.3 19.2 + - - -
219A ALA 2.9 14.4 - - - -
220A ASN* 4.3 0.9 - - - -
221A ILE* 5.1 0.6 - - - +
231A ILE* 1.3 79.4 - - - +
233A ILE* 1.3 60.5 + - - +
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Residues in contact with ILE 233 (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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67A MET* 4.1 26.0 - - + +
68A MET* 3.7 16.6 - - - +
71A VAL* 4.6 10.8 - - + -
72A PRO* 6.2 0.2 - - + -
189A VAL* 3.5 33.9 - - + -
190A ALA 3.5 4.5 - - - +
192A CYS* 4.4 0.9 - - - -
217A GLU 3.8 0.2 - - - +
218A TYR* 3.4 6.4 - - - -
219A ALA* 2.9 43.9 + - + +
221A ILE* 3.6 37.9 - - + -
232A GLY* 1.3 72.9 - - - +
234A LEU* 1.3 62.4 - - - +
235A CYS* 3.6 13.0 + - - -
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Residues in contact with LEU 234 (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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175A TYR* 3.4 30.3 - - + +
188A CYS 3.8 1.2 - - - +
189A VAL* 3.3 5.4 - - - -
190A ALA* 2.8 37.4 + - + +
192A CYS* 3.7 24.6 - - + +
205A MET* 3.9 27.4 - - + +
206A ILE* 3.5 34.8 - - + +
209A ALA* 4.1 8.5 - - + -
216A VAL* 3.7 13.9 - - + -
217A GLU 3.7 4.9 - - - +
218A TYR* 4.7 4.5 - - + -
233A ILE* 1.3 69.8 - - - +
235A CYS* 1.3 61.0 + - - +
236A CYS* 4.3 8.0 - - - -
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Residues in contact with CYS 235 (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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71A VAL* 4.5 4.0 - - - -
188A CYS 3.8 3.6 - - - -
189A VAL* 3.9 9.9 - - - -
215A LYS 3.5 1.5 - - - +
216A VAL* 3.2 8.1 - - - +
217A GLU* 2.6 49.4 + - + +
219A ALA* 4.7 0.2 - - - -
233A ILE* 3.8 28.7 - - - -
234A LEU* 1.3 76.9 - - - +
236A CYS* 1.3 59.4 + - - +
243A LEU* 3.5 18.6 - - + -
270A PHE* 3.7 33.2 - - + -
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Residues in contact with CYS 236 (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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175A TYR* 4.1 18.8 - - - -
187A TYR* 3.4 7.1 - - - -
188A CYS* 2.8 46.2 + - + +
209A ALA* 3.8 28.3 - - - -
213A PHE* 3.5 31.9 - - + -
215A LYS 3.6 3.1 - - - -
216A VAL* 4.7 1.1 - - - +
234A LEU* 4.3 12.8 - - - -
235A CYS* 1.3 76.9 - - - +
237A SER* 1.3 63.5 + - - +
243A LEU* 3.7 2.7 - - - +
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Residues in contact with SER 237 (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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186A GLY 4.3 1.1 - - - -
187A TYR* 3.3 28.1 - - - -
213A PHE* 3.4 9.2 - - - +
214A LYS 3.2 21.3 + - - -
215A LYS* 2.9 23.5 + - - -
217A GLU* 4.8 0.5 + - - -
236A CYS* 1.3 73.2 - - - +
238A LYS* 1.3 60.3 + - - +
239A THR 3.5 18.4 - - - -
242A GLY* 3.3 19.3 - - - -
243A LEU* 3.5 8.0 - - - +
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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