Contacts of the strand formed by residues 341 - 347 (chain A) in PDB entry 3HU1
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 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A ARG* 4.3 10.7 + - - +
293A ALA* 3.8 30.5 - - + +
294A GLU* 4.1 9.9 - - + +
297A ALA 5.0 0.9 - - - +
299A ALA* 3.5 13.7 - - + +
301A ILE* 3.8 34.1 - - + -
335A LEU* 4.0 32.3 - - + +
339A ALA* 3.4 15.2 - - + +
340A HIS* 1.3 82.8 - - - +
342A ILE* 1.3 69.6 + - - +
343A VAL 4.3 0.3 + - - -
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Residues in contact with ILE 342 (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 MET 4.2 7.2 - - - +
220A VAL* 4.0 28.7 - - + +
223A PRO* 4.8 11.2 - - + -
224A LEU* 3.8 30.1 - - + -
237A PRO* 5.0 7.2 - - + -
238A PRO 3.5 21.1 - - - +
239A ARG* 3.8 9.6 - - + +
241A ILE* 3.6 28.7 - - + -
299A ALA 3.2 6.7 + - - +
300A ILE* 3.4 5.6 - - - +
301A ILE 3.0 23.6 + - - +
340A HIS* 6.2 0.4 - - - -
341A VAL* 1.3 80.9 - - - +
343A VAL* 1.3 67.0 + - - +
344A MET* 4.0 1.6 + - + -
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Residues in contact with VAL 343 (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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239A ARG 3.0 13.9 + - - +
240A GLY* 3.2 4.2 - - - -
241A ILE 2.9 24.8 + - - -
290A PHE* 4.2 17.7 - - + -
301A ILE* 3.4 21.1 - - + +
303A ILE* 3.9 19.5 - - + -
332A MET* 3.9 22.0 - - + -
335A LEU* 4.3 14.8 - - + -
342A ILE* 1.3 75.2 - - - +
344A MET* 1.3 64.5 + - - +
363A PHE* 3.5 27.5 - - + -
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Residues in contact with MET 344 (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 ILE* 4.0 26.5 - - + -
220A VAL* 3.7 28.9 - - + -
241A ILE* 3.2 11.7 - - + +
243A LEU* 3.9 26.7 - - + -
254A ILE* 5.1 0.7 - - + -
258A VAL* 4.6 13.9 - - + -
300A ILE* 4.0 22.0 - - + -
301A ILE 2.7 13.5 + - - +
302A PHE* 3.6 34.3 - - + -
303A ILE* 2.8 31.6 + - - +
342A ILE* 4.0 1.5 + - + -
343A VAL* 1.3 77.7 - - - +
345A ALA* 1.3 56.5 + - - +
363A PHE* 4.2 0.2 - - - -
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Residues in contact with ALA 345 (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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241A ILE 2.9 6.3 + - - +
242A LEU* 3.4 7.0 - - + -
243A LEU* 2.6 35.7 + - - +
302A PHE* 4.4 4.5 - - - -
303A ILE* 3.1 17.7 - - + +
306A LEU* 3.8 25.1 - - + -
344A MET* 1.3 75.9 - - - +
346A ALA* 1.3 56.2 + - - +
363A PHE* 3.6 22.4 - - + -
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Residues in contact with ALA 346 (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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242A LEU* 4.8 1.1 - - - -
243A LEU* 3.2 8.1 - - + +
251A LYS* 3.8 25.4 - - + -
302A PHE* 3.8 16.6 - - + -
303A ILE 3.2 6.3 + - - -
304A ASP* 3.6 19.7 - - - +
305A GLU* 3.1 8.3 + - - -
306A LEU* 3.0 24.9 + - - +
345A ALA* 1.3 75.6 - - - +
347A THR* 1.3 61.1 + - - +
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Residues in contact with THR 347 (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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242A LEU* 4.0 14.8 - - + -
243A LEU 2.9 8.9 + - - +
244A TYR* 3.2 26.9 - - + +
245A GLY 3.5 0.3 + - - -
251A LYS* 3.4 12.0 - - - +
305A GLU* 5.0 1.8 - - - +
306A LEU* 4.7 0.4 - - - -
307A ASP* 3.0 28.7 + - - +
346A ALA* 1.3 75.8 - - - +
348A ASN* 1.3 67.0 + - - +
349A ARG 3.1 13.5 + - - -
350A PRO* 3.7 20.9 - - + -
353A ILE* 3.6 27.4 - - + -
800A AGS 4.8 0.7 - - - -
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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