Contacts of the strand formed by residues 316 - 323 (chain A) in PDB entry 2XHC
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 ALA 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A MET* 4.0 18.8 - - + -
305A VAL 3.7 5.4 - - - +
306A LYS* 4.5 4.7 - - + +
307A ILE* 4.1 2.4 - - - +
314A ASP 4.1 1.0 + - - -
315A PHE* 1.3 81.0 - - - +
317A GLY* 1.3 59.6 + - - +
333A VAL* 3.4 23.2 - - - +
334A THR 4.8 1.0 + - - -
352A ILE* 6.1 1.8 - - + -
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Residues in contact with GLY 317 (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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304A MET* 3.0 12.5 - - - +
305A VAL* 2.9 36.2 + - - -
307A ILE* 4.6 0.2 - - - -
316A ALA* 1.3 77.7 - - - +
318A VAL* 1.3 64.3 + - - -
331A VAL* 3.9 13.7 - - - -
332A ASN 3.2 12.8 - - - -
333A VAL* 4.7 0.2 - - - -
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Residues in contact with VAL 318 (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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302A GLY* 3.9 23.3 - - - +
303A ASP 3.5 2.7 - - - -
304A MET* 3.3 27.4 - - + -
317A GLY* 1.3 71.2 - - - -
319A ILE* 1.3 77.0 + - - +
320A LYS* 3.4 12.0 + - + +
331A VAL* 3.2 4.9 - - - +
332A ASN* 2.8 45.0 + - + +
339A GLU* 6.2 0.2 - - - +
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Residues in contact with ILE 319 (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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299A PHE* 3.4 35.9 - - + -
300A LYS 3.5 21.8 - - - +
301A VAL* 4.0 3.9 - - - +
302A GLY* 2.8 21.7 + - - -
303A ASP* 2.9 13.2 + - + +
305A VAL* 3.6 32.1 - - + -
317A GLY 4.3 0.6 - - - -
318A VAL* 1.3 77.8 - - - +
320A LYS* 1.3 63.6 + - - +
321A GLU 3.9 7.0 - - - +
322A ILE* 3.5 28.0 - - + -
329A LEU* 3.9 18.2 - - + -
330A LYS 4.0 3.6 - - - +
331A VAL* 4.2 4.7 - - + -
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Residues in contact with LYS 320 (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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301A VAL* 3.9 22.4 - - + +
318A VAL* 4.1 16.0 - - + +
319A ILE* 1.3 82.4 - - - +
321A GLU* 1.3 71.5 + - + +
330A LYS* 2.8 21.9 + - + +
332A ASN* 3.4 36.1 - - + +
339A GLU* 4.7 3.8 + - - -
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Residues in contact with GLU 321 (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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301A VAL* 5.0 1.8 - - - -
319A ILE* 3.9 2.1 - - - +
320A LYS* 1.3 80.9 - - - +
322A ILE* 1.3 70.3 + - - +
329A LEU* 3.5 3.5 - - - -
330A LYS* 2.8 75.8 + - + +
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Residues in contact with ILE 322 (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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299A PHE* 3.5 25.1 - - + +
300A LYS* 3.6 4.0 - - - -
301A VAL* 3.5 36.8 - - + +
319A ILE* 3.5 19.5 - - + -
321A GLU* 1.3 75.2 - - - +
323A ASP* 1.3 64.5 + - - +
324A PRO* 3.7 23.0 - - + +
328A GLU 3.9 3.8 - - - +
329A LEU* 3.6 15.9 - - + -
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Residues in contact with ASP 323 (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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322A ILE* 1.3 78.2 - - - +
324A PRO* 1.3 81.8 - - - +
325A GLU* 5.1 0.3 - - - +
326A ARG* 2.7 40.3 + - - +
327A GLN 3.1 15.1 + - - -
328A GLU* 3.0 30.5 + - + +
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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