Contacts of the strand formed by residues 314 - 319 (chain A) in PDB entry 4HNE
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 TRP 314 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ALA* 2.9 45.6 + - + +
274A LEU* 4.0 16.4 - - + -
290A LEU* 5.1 3.4 - - + -
294A PHE* 3.7 27.1 - + - -
297A LEU* 3.3 33.3 - - + +
309A ARG* 3.7 18.6 - - - +
310A GLY 2.9 21.7 + - - -
311A ASN* 3.1 24.7 + - - +
312A ASP 3.7 2.3 - - - +
313A ASN* 1.3 79.5 - - - +
315A LEU* 1.3 69.3 + - - +
316A ILE* 3.8 21.5 - - + -
342A VAL* 4.3 23.8 - - + -
343A ALA 3.7 10.3 - - - +
344A ALA* 4.8 0.2 - - - -
366A TRP* 4.4 3.3 - - + +
369A LEU* 3.8 24.2 - - + -
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Residues in contact with LEU 315 (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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264A VAL* 5.0 0.4 - - + -
267A TYR* 3.7 27.8 - - + -
268A LYS* 3.3 16.4 - - - +
269A ASP* 4.0 10.8 - - - +
270A ALA* 4.6 0.2 - - - -
312A ASP 4.0 13.0 - - - +
314A TRP* 1.3 85.5 - - - +
316A ILE* 1.3 63.3 + - - +
342A VAL* 3.1 9.9 - - - +
343A ALA* 2.9 34.5 + - + +
345A ILE* 3.5 44.9 - - + -
500A ADP 4.4 27.1 - - + +
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Residues in contact with ILE 316 (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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267A TYR* 3.8 2.5 - - - -
268A LYS 2.9 28.2 + - - -
270A ALA* 3.7 33.8 - - + +
273A TRP* 3.3 35.5 + - + -
274A LEU* 4.0 16.6 - - + -
277A PHE* 4.6 2.0 - - + -
290A LEU* 4.4 12.8 - - + -
314A TRP* 3.8 20.4 - - + -
315A LEU* 1.3 77.7 - - - +
317A LYS* 1.3 65.2 + - - +
318A TYR* 4.5 0.9 - - + +
340A ILE* 3.9 30.7 - - + -
341A LYS 3.3 5.8 - - - +
342A VAL* 4.6 2.0 - - + -
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Residues in contact with LYS 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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265A GLU 3.5 17.2 + - - -
266A GLY* 3.1 20.6 - - - +
267A TYR* 3.4 43.3 + - + +
273A TRP* 4.6 0.2 - - - +
316A ILE* 1.3 73.0 - - - +
318A TYR* 1.3 67.7 + - - +
319A ASP* 3.8 22.5 + - + +
339A VAL* 3.9 6.6 - - + +
340A ILE* 3.3 6.8 - - - +
341A LYS* 2.8 39.0 + - + +
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Residues in contact with TYR 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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266A GLY 4.6 1.4 + - - -
273A TRP* 3.7 58.6 - + + +
277A PHE* 3.9 12.1 - + + -
280A GLU* 4.2 12.0 + - - -
282A LEU* 3.4 23.7 - - + +
283A PRO* 4.5 8.8 - - - +
286A THR* 3.9 20.6 + - + +
316A ILE* 4.6 0.7 - - + -
317A LYS* 1.3 77.7 - - - +
319A ASP* 1.3 66.8 + - - +
320A CYS* 4.1 33.7 + - - +
338A PRO* 5.4 5.0 - - + +
339A VAL 3.7 14.8 - - - -
340A ILE* 4.1 17.7 - - + -
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Residues in contact with ASP 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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317A LYS* 3.8 27.0 + - + -
318A TYR* 1.3 75.6 - - - +
320A CYS* 1.3 67.6 + - - +
321A PRO* 3.7 10.1 - - + +
338A PRO* 4.0 2.6 - - - +
339A VAL* 3.4 42.8 + - - +
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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