Contacts of the strand formed by residues 314 - 319 (chain A) in PDB entry 5M5R
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 GLY 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A GLN* 4.7 4.0 - - - +
274A PHE* 3.9 15.0 - - - -
308A PRO* 3.7 7.6 - - - +
309A HIS* 3.0 21.8 + - - -
312A THR* 3.1 13.8 + - - -
313A ALA* 1.3 79.0 - - - +
315A ILE* 1.3 61.3 + - - +
327A VAL 3.3 12.8 - - - -
328A CYS* 4.0 5.4 - - - -
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Residues in contact with ILE 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ALA* 4.9 2.9 - - + -
264A MET* 4.7 2.2 - - - -
265A GLN* 3.4 41.1 - - + +
274A PHE* 4.0 23.3 - - + +
276A ILE* 3.8 33.4 - - + -
282A ILE* 4.6 1.1 - - + -
306A THR* 4.0 18.6 - - + +
307A ALA 3.7 5.2 - - - +
309A HIS* 4.0 3.3 - - - +
314A GLY* 1.3 74.5 - - - +
316A ILE* 1.3 64.4 + - - +
325A LEU* 5.8 0.3 - - - +
326A SER* 3.1 4.9 - - - -
327A VAL* 2.9 55.0 + - + +
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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
----------------------------------------------------------
12A HIS* 4.1 19.7 - - + +
32A MET* 3.6 12.5 - - + +
35A ASP* 4.0 26.9 - - + +
55A MET* 4.7 10.3 - - + -
276A ILE* 6.3 0.2 - - - -
306A THR* 3.2 6.5 - - - -
307A ALA* 2.9 51.4 + - + +
308A PRO 4.0 4.0 - - - +
309A HIS* 4.1 22.4 - - + +
315A ILE* 1.3 76.3 - - - +
317A GLY* 1.3 60.0 + - - +
324A VAL* 3.9 25.6 - - + -
325A LEU 3.3 12.1 - - - +
326A SER* 4.3 1.3 - - - -
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Residues in contact with GLY 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A MET* 3.8 4.5 - - - -
276A ILE* 6.2 1.1 - - - -
303A ILE* 4.7 4.5 - - - -
305A VAL 3.2 13.9 - - - -
306A THR* 4.1 5.6 - - - -
316A ILE* 1.3 75.8 - - - +
318A VAL* 1.3 64.3 + - - +
323A GLN 3.8 0.3 - - - +
324A VAL* 3.4 5.9 - - - +
325A LEU* 2.8 43.1 + - - +
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Residues in contact with VAL 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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15A LEU* 4.2 22.4 - - + -
30A LEU* 4.4 8.3 - - + -
32A MET* 4.0 19.1 - - - -
38A ILE* 4.3 7.0 - - + -
303A ILE* 3.7 7.3 - - - +
304A PHE* 3.3 37.2 + - + -
305A VAL* 3.2 27.5 + - + -
317A GLY* 1.3 78.2 - - - +
319A ASN* 1.3 72.9 + - - +
322A GLY* 4.2 4.0 - - - -
323A GLN 3.4 9.6 - - - +
324A VAL* 4.2 12.3 - - + -
325A LEU* 5.9 0.2 - - - -
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Residues in contact with ASN 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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25A ILE* 3.6 3.5 - - - +
299A SER* 3.1 26.6 + - - +
301A GLU* 3.9 16.1 - - + +
302A THR 3.2 14.6 - - - +
303A ILE* 4.0 8.3 - - + +
304A PHE* 3.8 3.6 - - - -
318A VAL* 1.3 84.4 - - - +
320A ARG* 1.3 59.1 + - - +
321A LYS* 3.2 13.4 + - - +
322A GLY* 2.9 19.2 + - - -
323A GLN* 3.0 55.7 + - - +
325A LEU* 4.4 2.5 - - + +
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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