Contacts of the strand formed by residues 312 - 317 (chain R) in PDB entry 5G04
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 VAL 312 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272R GLY* 4.5 2.9 - - - -
273R SER* 3.2 29.6 + - - +
284R GLY* 4.1 10.0 - - - -
285R SER 3.2 18.3 + - - +
288R GLY* 3.6 33.4 - - - +
290R ILE* 4.2 16.8 - - + -
308R HIS* 3.7 20.0 - - + -
311R GLU* 1.3 74.8 - - - +
313R CYS* 1.3 57.9 + - - +
314R GLY 3.5 21.3 - - - +
315R LEU* 4.5 2.2 - - + -
326R SER* 4.4 7.9 - - - -
327R GLY 3.6 7.2 - - - +
328R GLY* 4.4 0.4 - - - -
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Residues in contact with CYS 313 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186R TYR* 3.4 51.4 - - + +
188R ASN* 3.0 26.2 + - - +
273R SER* 4.4 1.1 - - - -
311R GLU* 4.1 1.6 - - - +
312R VAL* 1.3 74.4 - - - +
314R GLY* 1.3 56.8 + - - +
327R GLY 3.0 7.7 + - - -
328R GLY 4.0 15.5 - - - -
329R ASN* 4.0 4.3 - - - -
357R ALA* 4.8 2.7 - - - -
358R VAL 3.6 23.8 - - - -
359R LYS* 3.4 25.2 - - + +
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Residues in contact with GLY 314 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188R ASN* 5.2 1.1 - - - -
273R SER* 4.5 1.1 - - - -
312R VAL* 3.5 6.5 - - - +
313R CYS* 1.3 80.6 - - - +
315R LEU* 1.3 62.2 + - - +
316R ARG* 5.6 1.8 - - - -
325R ALA 4.5 0.2 - - - -
326R SER* 3.2 4.8 - - - -
327R GLY* 2.8 37.9 + - - +
358R VAL 4.3 1.8 - - - -
359R LYS 3.5 18.2 - - - -
361R VAL* 4.4 7.2 - - - -
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Residues in contact with LEU 315 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188R ASN* 6.2 0.2 - - - -
273R SER* 3.6 22.3 - - - +
274R LEU 3.8 2.9 - - - +
275R SER* 3.5 13.9 - - - +
282R SER* 3.5 34.5 - - - +
283R SER 3.7 2.0 - - - +
284R GLY* 3.5 23.8 - - - +
290R ILE* 3.9 22.2 - - + -
312R VAL* 4.5 1.6 - - + -
314R GLY* 1.3 72.7 - - - +
316R ARG* 1.3 83.1 + - - +
324R LEU* 3.9 23.6 - - + -
325R ALA 3.4 2.5 - - - -
326R SER* 3.8 24.5 - - - -
361R VAL* 5.0 1.6 - - - +
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Residues in contact with ARG 316 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188R ASN* 4.7 13.7 + - - -
274R LEU 4.5 7.7 + - - -
275R SER* 3.5 6.0 + - - -
314R GLY* 5.6 0.4 - - - -
315R LEU* 1.3 95.7 + - - +
317R TRP* 1.3 69.9 + - - +
324R LEU* 3.6 4.0 - - - +
325R ALA 2.8 36.5 + - - -
359R LYS 4.7 6.9 + - - -
360R ALA* 5.6 0.4 - - - +
361R VAL* 2.8 52.5 + - + +
362R ALA* 4.6 4.1 - - - +
363R TRP* 3.1 19.5 + - + +
404R SER* 6.2 2.6 - - - +
405R ILE 5.5 4.4 + - - +
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Residues in contact with TRP 317 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275R SER* 2.9 37.6 + - - +
276R TRP 3.6 18.8 - - - +
277R ASN* 3.4 40.8 - - + +
280R ILE* 4.5 9.2 - - + +
282R SER* 2.8 20.9 + - - +
292R HIS* 3.6 27.1 - + - -
316R ARG* 1.3 81.0 - - - +
318R ALA* 1.3 66.6 + - - +
319R PRO* 3.9 2.1 - - - +
321R GLY 3.5 18.6 - - - -
323R HIS 3.3 33.7 - - - -
324R LEU* 3.7 19.3 - - + +
337R PRO 4.5 2.2 - - - -
338R SER* 4.0 26.9 - - - -
363R TRP* 3.6 7.9 - - - -
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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