Contacts of the strand formed by residues 313 - 320 (chain A) in PDB entry 4RUH
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 SER 313 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A ARG* 3.6 4.8 + - - -
257A ILE* 3.9 6.7 - - - -
311A TYR 3.9 0.2 + - - -
312A PRO* 1.3 76.6 - - - +
314A LEU* 1.3 63.7 + - - +
315A SER* 5.2 0.3 + - - -
342A ILE* 3.3 7.6 - - - +
343A ARG* 2.9 51.7 + - - +
229B SER 4.5 0.2 + - - -
233B GLY* 3.5 37.6 + - - -
234B GLY* 3.8 6.5 - - - -
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Residues in contact with LEU 314 (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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250A LEU* 4.0 22.2 - - + +
251A VAL* 4.1 18.9 - - + +
257A ILE* 3.9 35.7 - - + +
259A ILE* 4.3 0.2 - - + -
313A SER* 1.3 77.2 - - - +
315A SER* 1.3 72.6 + - - +
316A LEU* 4.0 22.0 - - + -
340A PHE* 3.8 31.4 - - + -
341A SER 3.4 5.6 - - - +
342A ILE* 3.8 18.8 - - + -
233B GLY* 5.7 0.2 - - - -
238B GLU* 3.5 9.7 - - - +
241B THR* 5.3 2.6 + - - -
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Residues in contact with SER 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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313A SER* 5.2 0.7 + - - -
314A LEU* 1.3 74.4 + - - +
316A LEU* 1.3 61.9 + - - +
317A HIS* 3.3 23.1 + - - -
340A PHE* 3.1 5.6 - - - -
341A SER* 2.9 37.2 + - - -
229B SER* 4.0 13.9 + - - -
233B GLY* 4.2 7.3 - - - -
238B GLU* 2.8 34.5 + - - -
241B THR* 5.7 0.4 - - - -
332B ILE* 4.0 6.0 - - - +
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Residues in contact with LEU 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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247A MET* 4.0 32.3 - - + +
250A LEU* 3.6 31.6 - - + -
251A VAL* 5.6 5.2 - - + -
314A LEU* 4.0 9.2 - - + -
315A SER* 1.3 71.0 - - - +
317A HIS* 1.3 63.0 + - - +
318A GLY 3.6 0.7 - - - -
339A LYS 3.7 4.0 - - - -
340A PHE* 3.7 8.5 - - + -
238B GLU* 4.4 6.7 + - - +
240B MET* 3.6 23.6 - - + +
241B THR* 3.7 33.7 + - + +
244B ILE* 3.7 29.8 - - + -
245B LEU* 6.2 0.7 - - + -
331B VAL 4.6 0.5 - - - +
333B PRO* 4.3 5.7 - - - +
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Residues in contact with HIS 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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215A TYR* 3.2 37.4 - + - +
315A SER* 3.3 23.7 + - - -
316A LEU* 1.3 73.4 - - - +
318A GLY* 1.3 55.2 + - - +
339A LYS* 2.6 15.1 + - + +
340A PHE* 3.6 9.2 - - - -
341A SER* 2.4 29.7 + - - -
229B SER* 3.4 29.2 - - - -
240B MET* 4.2 3.1 - - - -
322B ALA* 3.5 4.7 - - - +
323B PHE* 3.1 29.9 + - + +
329B LYS 3.5 6.7 - - - +
330B THR* 4.1 3.4 - - - -
331B VAL 2.9 32.3 + - - +
333B PRO* 3.7 7.9 - - - +
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Residues in contact with GLY 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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247A MET* 3.8 3.8 - - - +
316A LEU 3.6 1.4 - - - -
317A HIS* 1.3 82.4 - - - +
319A ILE* 1.3 63.4 + - - +
338A GLY* 3.5 2.3 - - - -
339A LYS* 2.8 32.5 + - - +
240B MET* 3.6 17.3 - - - +
322B ALA* 3.8 6.5 - - - -
323B PHE 3.4 11.2 - - - -
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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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240A MET* 3.8 22.0 - - + -
243A LEU* 3.8 34.5 - - + -
244A ILE* 4.4 9.4 - - + -
247A MET* 4.1 9.2 - - + -
318A GLY* 1.3 79.5 - - - +
320A GLU* 1.3 72.7 + - - +
321A GLY 4.0 0.2 + - - -
322A ALA* 4.0 17.4 + - + +
324A SER* 5.4 1.0 - - - -
336A VAL* 3.9 12.6 - - + -
337A VAL 3.4 5.4 - - - +
339A LYS* 5.6 0.7 - - - -
319B ILE* 4.0 33.9 - - + +
322B ALA* 5.0 1.6 - - - +
323B PHE 3.4 4.9 + - - -
324B SER* 3.3 22.9 - - - -
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Residues in contact with GLU 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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217A PHE* 5.6 0.2 - - - -
319A ILE* 1.3 73.8 - - - +
321A GLY* 1.3 65.1 + - - +
322A ALA 3.5 0.6 + - - -
335A LYS 4.1 0.5 - - - +
336A VAL* 3.5 4.9 - - - -
337A VAL* 2.7 48.7 + - + +
339A LYS* 2.5 38.1 + - - +
324B SER* 3.4 11.9 - - - +
325B GLY 3.4 19.1 - - - +
326B SER* 3.6 19.2 + - - -
327B GLY 4.1 2.1 + - - -
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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