Contacts of the strand formed by residues 236 - 244 (chain A) in PDB entry 1HLE
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 LYS 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A TYR* 3.2 30.0 + - - +
232A ILE 2.9 7.6 + - - -
233A GLU 3.3 11.5 + - - +
234A ASP 5.0 2.0 - - - +
235A LEU* 1.3 80.5 - - - +
237A CYS* 1.3 51.0 + - - +
255A PRO* 3.6 3.1 - - - +
256A ASP* 2.7 49.6 + - + +
258A GLU* 4.3 24.4 - - + +
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Residues in contact with CYS 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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231A TYR* 3.4 6.2 - - - -
232A ILE* 2.6 45.2 + - + +
235A LEU* 3.9 22.4 - - + +
236A LYS* 1.3 77.0 - - - +
238A ARG* 1.3 73.3 + - - +
253A LEU* 4.2 14.4 - - - -
254A LEU 3.4 18.6 - - - -
255A PRO* 4.2 0.4 - - + -
256A ASP 4.3 0.4 - - - +
263A ILE* 3.4 32.1 - - + -
275A TRP* 6.4 1.1 - - - -
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Residues in contact with ARG 238 (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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229A TYR* 3.1 31.8 + - + +
230A ASN 3.4 3.8 - - - +
231A TYR* 3.5 17.0 - - + -
237A CYS* 1.3 75.7 - - - +
239A VAL* 1.3 63.5 + - - +
252A ILE 3.6 1.0 - - - +
253A LEU* 3.5 3.8 - - - -
254A LEU* 2.8 42.0 + - + +
255A PRO 5.1 1.0 + - - -
256A ASP* 2.8 44.9 + - - +
362B GLU* 5.2 2.6 + - - -
363B ASN* 3.1 31.9 + - - +
364B PHE* 3.6 23.5 - - + +
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Residues in contact with VAL 239 (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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229A TYR* 3.4 9.4 - - - -
230A ASN 2.8 33.8 + - - +
232A ILE* 3.7 33.2 - - + -
237A CYS* 5.1 0.9 - - - -
238A ARG* 1.3 77.3 - - - +
240A LEU* 1.3 65.9 + - - +
251A ILE* 3.9 25.4 - - + -
252A ILE 3.3 3.1 - - - +
253A LEU* 3.6 23.1 - - + -
275A TRP* 3.8 18.4 - - + +
276A THR* 4.1 1.8 - - + -
279A LEU* 4.1 17.0 - - + -
364B PHE* 4.2 0.9 - - - -
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Residues in contact with LEU 240 (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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227A PHE* 3.6 34.5 - - + -
228A PRO 3.7 7.2 - - - +
229A TYR* 4.6 3.6 - - + -
239A VAL* 1.3 80.7 - - - +
241A GLU* 1.3 59.5 + - - +
242A LEU* 3.9 30.1 - - + -
250A MET 3.6 1.0 - - - +
251A ILE* 3.3 5.4 - - - +
252A ILE* 2.9 36.3 + - + +
279A LEU* 5.0 0.4 - - - -
284A VAL* 4.4 18.8 - - + -
286A VAL* 3.9 17.7 - - + -
364B PHE* 3.6 41.0 - - + -
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Residues in contact with GLU 241 (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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227A PHE* 3.7 10.0 - - - +
228A PRO* 3.2 40.5 + - + +
240A LEU* 1.3 74.0 - - - +
242A LEU* 1.3 64.3 + - - +
243A PRO* 3.5 15.0 - - + +
249A SER* 2.6 35.3 + - - +
250A MET 3.4 3.4 - - - -
251A ILE* 3.7 11.0 - - + -
277A PRO* 5.1 6.9 - - - +
279A LEU* 3.6 24.1 - - + +
375B ARG* 3.4 22.2 + - - -
377B ASN* 4.2 2.6 + - - -
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Residues in contact with LEU 242 (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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194A TRP* 3.6 31.8 - - + -
196A GLN 6.1 0.4 - - - +
198A PHE* 4.8 11.2 - - + -
223A GLN* 5.5 0.2 - - - +
227A PHE* 3.7 36.6 - - + -
240A LEU* 3.9 24.5 - - + -
241A GLU* 1.3 74.3 - - - +
243A PRO* 1.4 68.4 - - - +
244A TYR* 3.7 0.3 + - - -
249A SER* 4.4 0.9 - - - -
250A MET* 2.8 33.7 + - + +
252A ILE* 3.9 25.6 - - + -
286A VAL* 4.8 4.7 - - + -
288A LEU* 4.0 18.2 - - + -
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Residues in contact with PRO 243 (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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194A TRP* 3.9 7.3 - - - +
195A GLN* 3.0 40.7 + - + +
196A GLN 4.5 0.5 + - - -
227A PHE* 4.1 17.5 - - + -
228A PRO* 4.8 9.2 - - + -
241A GLU* 3.5 17.9 - - + +
242A LEU* 1.4 86.0 - - - +
244A TYR* 1.3 64.3 + - - +
246A LYS* 4.1 23.8 - - + -
249A SER* 3.7 17.7 - - - +
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Residues in contact with TYR 244 (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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110A TYR* 5.8 1.8 - - + -
190A PHE* 3.8 33.2 - + + -
192A GLY* 3.7 16.4 - - - -
193A ASN 3.4 17.7 - - - +
194A TRP* 3.4 29.0 - + - -
195A GLN* 3.7 7.4 - - - +
243A PRO* 1.3 76.1 - - - +
245A GLN* 1.3 64.1 + - - +
246A LYS* 2.9 23.9 + - - -
248A LEU* 3.0 34.1 + - + +
249A SER* 3.8 4.9 - - - -
250A MET* 3.4 33.9 - - + +
345A THR* 2.8 38.6 + - - +
374B ILE* 4.1 7.0 - - + +
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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