Contacts of the strand formed by residues 340 - 347 (chain A) in PDB entry 2HD5
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 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A ASP* 5.3 3.7 - - - +
331A SER* 3.7 27.4 - - - -
332A LEU 3.3 4.3 - - - -
333A THR* 3.4 23.3 - - + +
338A GLY 3.4 3.4 + - - +
339A TYR* 1.3 93.8 + - - +
341A SER* 1.3 59.6 + - - +
342A THR* 3.7 14.2 + - - -
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Residues in contact with SER 341 (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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330A SER 3.6 1.4 - - - +
331A SER* 3.6 1.4 - - - -
332A LEU* 2.6 48.0 + - - +
339A TYR* 3.7 24.8 + - - -
340A CYS* 1.3 72.5 - - - +
342A THR* 1.3 60.9 + - - +
343A VAL* 5.3 0.7 - - - +
382A CYS* 4.8 7.2 - - - -
64B GLU* 2.8 32.2 + - - +
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Residues in contact with THR 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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313A LYS* 2.5 67.4 + - + +
329A LYS* 3.7 20.4 - - + -
330A SER 3.3 3.8 - - - +
331A SER* 3.7 12.3 + - - -
339A TYR* 5.4 1.2 + - - -
340A CYS* 3.7 11.2 + - - -
341A SER* 1.3 75.7 + - - +
343A VAL* 1.3 68.7 + - - +
344A PHE* 3.3 34.8 - - + -
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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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313A LYS* 4.8 5.2 - - + -
329A LYS* 3.6 2.1 - - - -
330A SER* 2.7 51.5 + - - +
341A SER* 5.3 1.1 - - - +
342A THR* 1.3 79.3 - - - +
344A PHE* 1.3 67.6 + - - +
345A ASP* 4.3 12.9 + - - +
62B GLN* 6.0 2.5 - - + -
63B LYS 3.6 22.0 - - - +
64B GLU* 3.4 39.9 - - + +
65B SER* 4.7 1.3 - - - +
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Residues in contact with PHE 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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313A MET* 3.4 88.9 + - + +
327A GLN* 3.4 28.0 + - - +
328A LEU 3.2 14.8 - - - +
329A LYS* 3.6 16.2 - - + -
342A THR* 3.3 27.4 - - + -
343A VAL* 1.3 79.5 - - - +
345A ASP* 1.3 65.1 + - - +
346A PRO* 4.2 4.2 - - - +
396A GLN* 3.3 33.2 - - + -
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Residues in contact with ASP 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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327A GLN* 4.4 2.9 - - - -
328A LEU* 2.8 42.9 + - + +
330A SER* 5.3 1.4 - - - -
343A VAL* 4.4 10.9 + - - +
344A PHE* 1.3 79.1 - - - +
346A PRO* 1.3 75.0 - - + +
393A PHE* 4.7 7.5 - - - -
45B PHE* 3.6 20.5 - - + -
65B SER* 3.4 22.0 + - - -
66B THR* 3.1 32.4 + - - +
68B HIS* 5.5 1.2 + - - +
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Residues in contact with PRO 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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313A TRP* 4.4 5.6 - - + +
314A TYR* 3.5 59.0 - - + +
315A ARG* 5.7 0.2 - - - +
325A VAL* 4.4 2.2 - - + -
326A GLY 3.3 12.3 - - - +
327A GLN* 4.3 2.4 - - + -
328A LEU* 5.5 0.2 - - - +
344A PHE 4.2 4.7 - - - +
345A ASP* 1.3 92.3 - - + +
347A PHE* 1.3 61.0 + - - +
348A TRP* 5.4 0.2 - - + -
45B PHE* 4.8 6.3 - - + -
46B ALA* 3.2 35.8 + - + -
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Residues in contact with PHE 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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325A VAL* 3.3 3.6 - - - +
326A GLY* 2.8 49.0 + - - -
327A GLN 3.3 27.4 - - - -
328A LEU* 3.6 33.9 - - + -
346A PRO* 1.3 74.5 - - - +
348A TRP* 1.3 65.2 + - - +
349A ASP* 3.4 29.8 - - - +
350A LEU* 3.7 26.9 - - + -
395A ILE* 4.4 10.5 - - + -
397A ARG 4.0 3.1 - - - -
399A PRO* 3.9 30.1 - - + -
402A LEU* 4.1 7.6 - - + -
46B ALA* 4.4 4.5 - - - +
47B GLY 4.5 1.1 - - - +
68B HIS* 6.2 1.8 - - + +
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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