Contacts of the strand formed by residues 293 - 298 (chain A) in PDB entry 4L59
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 ARG 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A ASN* 3.2 8.0 + - - -
290A CYS 2.9 32.7 + - - +
291A GLY 3.2 0.4 - - - -
292A TYR* 1.3 81.4 - - - +
294A ILE* 1.3 64.0 + - - +
308A TRP* 3.4 42.1 + - + +
309A VAL 3.3 10.3 + - - +
310A ASN* 3.5 23.3 + - - +
311A ALA 4.2 0.7 - - - +
484A VAL* 3.7 27.4 - - - +
489A PRO* 2.8 29.3 + - - +
490A MET* 3.5 9.9 + - - +
492A ILE* 4.1 14.8 - - - +
526A ASP* 4.7 4.2 + - - -
532A TRP* 4.1 8.7 - - + -
538A HIS* 3.3 36.0 + - + -
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Residues in contact with ILE 294 (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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262A ASN* 3.7 10.1 - - - +
264A PHE* 3.6 49.4 - - + -
270A LEU* 5.2 0.2 - - + -
286A VAL* 4.5 6.7 - - + -
288A GLU 3.4 9.9 - - - +
289A VAL* 4.4 5.2 - - + -
293A ARG* 1.3 79.5 - - - +
295A LYS* 1.3 59.8 + - - +
296A LEU* 3.8 23.5 + - + -
307A PHE 3.7 0.3 - - - +
308A TRP* 3.3 8.8 - - - -
309A VAL* 2.9 55.0 + - + +
310A ASN 4.9 1.8 - - - +
311A ALA* 4.9 4.3 - - + -
316A ILE* 4.2 15.3 - - + -
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Residues in contact with LYS 295 (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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286A VAL* 3.8 2.8 - - - -
287A ALA* 2.8 32.7 + - + +
288A GLU* 2.9 47.8 + - + +
294A ILE* 1.3 72.3 - - - +
296A LEU* 1.3 63.5 + - - +
306A ASP* 4.0 34.2 + - + +
307A PHE 3.3 9.9 - - - +
308A TRP* 3.6 27.1 - - + +
607A UNX 3.2 25.6 - - - -
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Residues in contact with LEU 296 (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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270A LEU* 4.2 13.2 - - + -
284A LEU* 3.9 13.9 - - + -
285A THR 3.6 9.6 - - - +
286A VAL* 4.1 14.1 - - + -
294A ILE* 3.8 24.9 - - + +
295A LYS* 1.3 81.4 - - - +
297A HIS* 1.3 58.9 + - - +
306A ASP* 3.2 10.6 - - - +
307A PHE* 2.7 70.2 + - + +
309A VAL* 3.9 14.6 - - + -
316A ILE* 3.8 26.7 - - + -
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Residues in contact with HIS 297 (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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284A LEU* 3.2 8.3 - - - -
285A THR* 2.8 42.9 + - + +
287A ALA* 4.0 16.2 - - + -
296A LEU* 1.3 75.0 - - - +
298A PHE* 1.3 79.3 + - - +
299A ASP* 3.4 15.5 + - - -
300A GLY 4.2 3.2 + - - -
301A TYR 3.1 26.0 + - - -
302A SER 4.2 0.7 - - - -
303A ASP* 3.1 24.1 + - - -
306A ASP* 2.8 24.1 + - - +
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Residues in contact with PHE 298 (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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273A VAL 4.9 0.4 - - - -
274A ASP* 3.6 31.0 - - + -
275A PRO* 4.0 1.8 - - + -
282A CYS* 3.6 30.7 - - + -
283A VAL 3.8 4.0 - - - +
284A LEU* 3.4 19.1 - - + -
297A HIS* 1.3 82.7 + - - +
299A ASP* 1.3 66.5 + - - +
301A TYR* 3.0 36.7 + + + +
305A TYR* 3.5 30.9 - + + +
306A ASP* 4.4 0.8 + - - -
307A PHE* 3.5 27.1 - + - -
601A 1VZ 3.6 28.3 - - + -
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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