Contacts of the strand formed by residues 233 - 238 (chain A) in PDB entry 1H7B
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 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A VAL 2.9 10.6 + - - +
196A THR* 3.5 25.8 - - + +
197A ILE 2.9 25.1 + - - -
231A PHE* 4.0 12.8 - - + +
232A PRO* 1.3 75.9 - - - +
234A LEU* 1.3 62.4 + - - +
235A VAL* 4.2 2.7 - - + -
266A TYR* 3.0 39.3 - - + +
268A ASP* 5.0 1.4 + - - +
289A GLY 5.7 0.2 - - - -
290A CYS* 2.5 53.3 + - - +
291A ARG* 4.5 5.1 - - - +
507A TYR* 5.1 1.4 + - - -
533A TYR* 4.6 11.4 + - - +
577A ARG* 6.0 0.6 - - - +
580A ALA 3.9 12.3 + - - -
581A TYR* 4.1 15.9 - - - -
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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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179A GLU* 5.2 0.9 - - - +
197A ILE* 3.5 17.5 - - + -
199A PHE* 4.3 5.8 - - + -
214A ILE* 3.8 29.4 - - + -
215A LEU* 4.6 13.2 - - + -
218A ARG* 3.4 57.7 - - + +
232A PRO* 3.5 5.8 + - + +
233A LYS* 1.3 79.6 - - - +
235A VAL* 1.3 63.6 + - - +
266A TYR* 3.7 18.2 - - + -
267A PRO* 3.1 16.1 - - + +
268A ASP 2.9 21.1 + - - -
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Residues in contact with VAL 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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196A THR* 4.0 21.8 - - + -
197A ILE 3.1 6.5 + - - +
198A THR* 3.1 18.6 - - + -
199A PHE* 3.1 26.8 + - - +
233A LYS* 5.1 2.2 - - + -
234A LEU* 1.3 80.9 - - - +
236A MET* 1.3 61.7 + - - +
237A PHE* 5.5 1.1 - - + -
267A PRO* 4.5 0.4 - - - -
268A ASP* 3.3 10.8 - - + +
269A ILE 4.3 1.1 - - - -
270A ILE* 3.7 37.0 - - + +
287A PRO* 4.4 2.9 - - + -
533A TYR* 3.3 35.0 - - + +
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Residues in contact with MET 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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199A PHE* 3.1 44.4 - - + +
200A GLY* 4.0 2.5 - - - -
211A GLN* 3.9 5.2 - - - +
215A LEU* 3.7 9.2 - - + -
235A VAL* 1.3 75.6 - - - +
237A PHE* 1.3 76.4 + - - +
238A VAL* 4.6 7.4 - - + -
243A ASN* 4.2 13.2 - - - +
253A ILE* 3.4 31.9 - - + -
254A LYS* 4.7 5.4 - - - -
257A ALA* 3.7 20.0 - - + -
267A PRO* 4.3 7.6 - - + +
268A ASP 2.9 11.0 + - - +
269A ILE* 3.2 10.2 - - + +
270A ILE 2.9 23.9 + - - -
524A TRP* 5.4 2.2 - - - -
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Residues in contact with PHE 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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131A ASN* 3.3 24.5 - - - -
198A THR* 3.8 11.0 - - - -
199A PHE 2.8 17.0 + - - +
200A GLY* 3.9 1.6 - - - -
201A THR* 3.5 34.8 - - + -
235A VAL* 5.5 1.1 - - + -
236A MET* 1.3 88.2 - - - +
238A VAL* 1.3 59.6 + - - +
239A GLU* 4.2 0.4 - - + -
243A ASN* 2.8 17.9 + - - +
270A ILE* 3.5 42.6 - - + -
272A ALA* 5.0 7.0 - - + -
284A PRO* 3.4 30.5 - - + -
285A VAL 4.2 2.9 - - - -
286A SER* 3.6 32.8 - - - -
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Residues in contact with VAL 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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236A MET* 4.2 16.2 - - + +
237A PHE* 1.3 81.0 - - - +
239A GLU* 1.3 60.6 + - - +
243A ASN* 3.5 16.6 - - + +
244A LEU* 4.7 12.0 - - + +
254A LYS* 5.7 6.3 - - + -
269A ILE* 4.2 24.2 - - + -
270A ILE 3.1 14.5 + - - +
271A SER* 3.9 4.5 - - - -
272A ALA 3.2 18.3 + - - +
273A LYS 4.7 0.7 + - - -
524A TRP* 5.2 7.4 - - + -
528A ALA* 4.1 26.2 - - + -
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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