Contacts of the strand formed by residues 302 - 309 (chain A) in PDB entry 4R54
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 THR 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLN* 3.6 30.5 - - + +
135A VAL* 4.0 16.2 - - + +
136A ALA 4.8 0.7 - - - +
278A GLY 2.9 15.4 + - - -
279A ALA* 3.3 3.3 - - - +
280A VAL* 2.8 25.5 + - - -
301A ASP* 1.3 73.2 - - - +
303A PHE* 1.3 64.3 + - - +
304A VAL* 4.1 6.1 + - + +
321A VAL* 3.7 19.1 - - + -
322A VAL 3.6 7.9 - - - +
323A SER* 3.4 13.3 + - - -
328A LYS* 3.8 15.9 - - - +
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Residues in contact with PHE 303 (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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280A VAL* 3.4 33.7 - - + +
282A GLU* 3.4 41.3 - - - +
291A PRO* 3.4 14.9 - - + +
292A GLN 6.3 0.2 - - - -
295A ASN 5.1 2.9 - - - -
296A ALA* 3.9 31.4 - - + -
299A SER* 3.5 25.1 - - - -
301A ASP* 3.7 21.1 - - + -
302A THR* 1.3 71.0 - - - +
304A VAL* 1.3 62.4 - - - +
321A VAL* 3.3 4.9 - - - +
322A VAL 2.8 44.6 + - - +
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Residues in contact with VAL 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA* 3.7 24.2 - - + -
273A ILE* 4.0 26.5 - - + -
279A ALA* 4.9 1.8 - - + -
280A VAL 3.0 6.2 + - - +
281A LEU* 3.6 8.5 - - - +
282A GLU 2.9 22.7 + - - +
291A PRO* 3.5 4.2 - - - +
302A THR* 4.3 9.6 - - + +
303A PHE* 1.3 82.0 - - - +
305A GLY* 1.3 61.2 + - - +
307A ILE* 3.9 21.5 - - + -
319A MET* 3.9 24.0 - - + -
320A TRP 3.3 9.4 - - - +
321A VAL* 4.2 6.1 - - + -
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Residues in contact with GLY 305 (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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282A GLU 3.4 14.8 - - - -
283A ASP* 3.4 11.7 - - - -
291A PRO* 3.4 5.7 - - - +
304A VAL* 1.3 75.5 - - - +
306A ARG* 1.3 66.4 + - - -
307A ILE* 2.9 8.0 + - - +
319A MET* 3.5 2.8 - - - -
320A TRP* 2.8 34.7 + - - -
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Residues in contact with ARG 306 (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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282A GLU 4.6 0.8 + - - -
283A ASP* 3.4 11.8 + - - -
285A VAL* 4.6 5.5 - - - +
290A TYR* 4.2 17.5 - - + +
305A GLY* 1.3 70.7 - - - +
307A ILE* 1.3 61.8 + - - +
308A ARG* 2.8 46.7 + - - +
318A HIS 3.3 3.8 - - - +
319A MET* 3.7 0.2 - - - -
320A TRP* 3.8 22.0 - - + +
207B PRO* 3.1 41.3 + - + +
212B PHE* 3.5 28.7 - - - -
216B ASP 2.9 23.6 + - - -
217B TYR* 3.8 1.0 - - - +
218B THR* 4.4 1.8 - - - +
221B GLU* 2.9 41.2 + - - -
242B THR* 4.5 6.3 - - + +
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Residues in contact with ILE 307 (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 ILE* 4.0 22.6 - - + +
269A VAL* 4.2 16.4 - - + -
270A LYS* 4.1 26.6 + - + -
273A ILE* 3.7 27.8 - - + -
281A LEU* 3.7 28.3 - - + -
283A ASP* 2.9 17.2 + - - +
304A VAL* 3.9 7.9 - - + -
305A GLY* 2.9 13.2 - - - +
306A ARG* 1.3 75.3 - - - +
308A ARG* 1.3 63.7 + - - +
317A ILE* 4.3 8.1 - - + -
318A HIS 3.3 4.5 - - - +
319A MET* 3.8 12.3 - - + -
216B ASP* 5.1 7.1 - - - +
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Residues in contact with ARG 308 (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 ILE* 3.6 12.6 - - - -
306A ARG* 2.8 54.8 + - - +
307A ILE* 1.3 75.6 - - - +
309A LYS* 1.3 63.9 + - - +
317A ILE* 3.4 3.3 - - - +
318A HIS* 2.8 51.4 + - + +
319A MET* 4.3 2.2 - - - +
215B ASN 4.8 1.8 - - - +
216B ASP* 3.5 33.0 - - + +
217B TYR* 3.2 34.9 - - + +
221B GLU* 4.0 2.8 + - - -
241B ALA 2.8 27.7 + - - -
242B THR* 2.8 27.9 + - - +
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Residues in contact with LYS 309 (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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263A VAL* 4.4 16.1 - - - +
264A ALA 4.3 15.2 + - - -
265A PRO* 4.5 3.6 - - - +
266A ILE* 3.6 33.3 - - + +
308A ARG* 1.3 75.1 - - - +
310A ASP* 1.3 64.1 + - - +
311A LEU* 4.7 0.9 - - - +
313A ALA 5.8 0.2 - - - +
314A GLU* 4.6 14.8 + - - +
316A GLY 3.6 9.0 - - - +
317A ILE* 5.5 0.9 - - + -
318A HIS* 4.4 0.2 - - - -
217B TYR* 2.7 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