Contacts of the strand formed by residues 234 - 243 (chain A) in PDB entry 1H6T
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 VAL 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A GLN 2.9 5.9 + - - +
212A ASN* 3.4 23.2 - - - +
213A LEU 2.9 23.7 + - - -
214A TYR* 3.7 35.9 - - + +
232A LEU* 4.1 3.6 - - - +
233A ASP* 1.3 85.0 - - + +
235A LEU* 1.3 66.3 + - - +
236A GLU* 4.8 6.1 - - + +
307A ALA* 4.6 0.7 - - - -
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Residues in contact with LEU 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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213A LEU* 3.3 39.5 - - + +
226A LEU* 4.4 4.9 - - + -
232A LEU* 4.1 11.4 - - + -
233A ASP 4.3 0.6 - - - -
234A VAL* 1.3 77.6 - - - +
236A GLU* 1.3 64.8 + - - +
237A LEU* 3.7 33.0 - - + -
302A VAL* 4.1 4.9 - - + -
304A ILE* 3.9 28.0 - - + +
307A ALA* 4.1 17.1 - - + +
308A LYS 4.0 5.5 + - - +
309A ALA* 3.1 34.8 - - + +
310A ARG 5.0 0.3 + - - -
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Residues in contact with GLU 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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194A GLU* 4.0 11.4 - - - +
213A LEU 3.0 7.8 + - - +
214A TYR* 3.6 39.7 - - + -
215A LEU* 2.8 33.7 + - - +
216A SER* 3.2 6.5 + - - -
234A VAL* 4.8 5.9 - - + +
235A LEU* 1.3 75.7 - - - +
237A LEU* 1.3 62.1 + - - +
238A PHE* 3.5 36.0 - - + -
310A ARG 6.0 0.2 - - - +
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Residues in contact with LEU 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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201A ILE* 5.5 0.2 - - + -
215A LEU* 3.9 34.1 - - + -
216A SER* 4.3 0.4 - - - +
220A ILE* 4.6 8.1 - - + -
223A LEU* 4.0 35.0 - - + -
226A LEU* 3.9 12.8 - - + -
235A LEU* 3.7 31.8 + - + -
236A GLU* 1.3 74.7 - - - +
238A PHE* 1.3 63.2 + - - +
240A GLN* 3.1 22.6 + - - +
302A VAL* 4.5 3.1 - - + -
309A ALA* 4.4 6.3 - - + -
310A ARG 3.2 17.3 + - - +
311A PHE* 3.7 11.8 - - + -
312A HIS 3.3 14.7 + - - +
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Residues in contact with PHE 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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216A SER* 3.2 22.8 - - - -
217A LYS* 3.0 33.9 + - - -
236A GLU* 3.5 43.7 - - + -
237A LEU* 1.3 83.0 - - - +
239A SER* 1.3 80.6 + - - +
240A GLN* 3.2 2.2 + - - -
310A ARG* 3.3 48.9 + - + +
312A HIS* 3.7 7.4 - - + +
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Residues in contact with SER 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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217A LYS* 3.3 39.8 + - - +
238A PHE* 1.3 85.9 - - - +
240A GLN* 1.3 65.9 + - - +
241A GLU* 3.7 12.0 + - - +
310A ARG* 5.6 0.5 + - - -
312A HIS* 3.0 32.1 + - - -
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Residues in contact with GLN 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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215A LEU 3.0 24.2 + - - -
216A SER* 3.8 0.8 - - - +
218A ASN* 2.9 35.8 + - - +
220A ILE* 3.1 42.4 + - - +
237A LEU* 3.1 28.2 + - - +
238A PHE 3.5 5.7 + - - -
239A SER* 1.3 79.9 - - - +
241A GLU* 1.3 63.7 + - - +
242A CYS* 4.2 2.5 - - - -
298A PHE* 4.0 8.1 - - + -
311A PHE* 4.0 7.6 - - + -
312A HIS 3.0 18.0 + - - +
313A GLY* 3.1 1.4 - - - -
314A ARG 2.9 23.3 + - - -
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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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218A ASN 3.0 7.1 + - - +
219A HIS* 2.7 46.7 + - + +
239A SER* 4.2 10.9 - - - +
240A GLN* 1.3 81.6 - - - +
242A CYS* 1.3 62.2 + - - +
243A LEU 4.1 1.2 + - - -
314A ARG* 3.0 53.1 + - - +
316A THR* 4.3 5.0 + - - -
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Residues in contact with CYS 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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219A HIS* 3.9 13.9 - - - +
220A ILE 3.8 22.4 - - - -
221A SER* 3.9 19.7 - - - -
240A GLN* 4.5 2.5 - - - -
241A GLU* 1.3 78.8 + - - +
243A LEU* 1.3 61.1 + - - +
244A ASN* 3.9 3.5 + - - +
298A PHE* 4.3 11.4 - - - -
314A ARG 2.8 15.3 + - - +
315A VAL* 3.3 17.2 - - + +
316A THR* 2.9 26.7 + - - +
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Residues in contact with LEU 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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219A HIS* 5.8 1.5 + - + -
241A GLU 4.1 1.8 + - - -
242A CYS* 1.3 71.0 - - - +
244A ASN* 1.3 68.9 + - - +
245A LYS* 4.0 0.7 + - - +
293A GLU* 5.6 0.2 - - - +
316A THR* 3.8 20.9 - - + +
318A PRO* 3.8 28.0 - - + -
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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