Contacts of the helix formed by residues 315 - 325 (chain A) in PDB entry 4WCX
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 LYS 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A GLU* 1.3 75.5 + - - +
316A PRO* 1.3 65.8 - - + +
317A LYS* 3.3 4.0 - - + +
318A PHE* 3.2 13.1 + - + +
319A ARG* 2.8 31.1 + - - +
358A GLU* 4.1 18.1 + - + +
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Residues in contact with PRO 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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315A LYS* 1.3 87.8 - - + +
317A LYS* 1.3 61.2 + - - +
319A ARG* 3.5 8.2 - - + +
320A GLU* 3.3 21.7 + - - +
358A GLU 3.8 12.3 - - - +
359A ASP* 3.8 15.9 - - + +
360A LYS 5.3 0.4 - - - +
361A ARG* 3.8 45.4 + - + +
373A GLN* 5.6 0.2 + - - -
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Residues in contact with LYS 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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315A LYS* 3.2 2.3 + - + +
316A PRO* 1.3 76.4 - - - +
318A PHE* 1.3 65.6 + - - +
320A GLU* 3.4 8.1 + - - +
321A GLU* 3.3 19.7 + - - +
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Residues in contact with PHE 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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271A ARG* 3.3 22.2 - - - -
289A ASP* 3.5 51.4 - - + +
292A PHE* 3.7 12.1 - + - -
293A LYS* 4.7 4.7 - - + -
314A GLU* 3.4 21.8 - - + +
315A LYS* 3.2 14.0 + - + +
317A LYS* 1.3 76.6 - - - +
319A ARG* 1.3 67.9 + - - +
321A GLU* 3.0 28.9 + - - +
322A VAL* 2.9 47.5 + - + +
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Residues in contact with ARG 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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310A LEU* 2.9 41.7 + - + +
311A SER 2.9 24.8 + - - -
312A THR* 3.5 6.4 - - - +
314A GLU* 3.6 31.8 - - + +
315A LYS 2.8 11.5 + - - +
316A PRO* 3.5 7.4 - - + +
318A PHE* 1.3 78.1 - - - +
320A GLU* 1.3 58.3 + - - +
322A VAL* 3.3 0.7 + - - -
323A ILE* 2.9 41.6 + - + +
330A ILE* 3.6 18.4 - - - +
331A SER* 2.8 35.5 + - - +
359A ASP* 2.9 33.1 + - - -
361A ARG* 5.1 2.0 - - - +
366A ILE* 4.2 4.9 - - - +
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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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316A PRO 3.3 10.0 + - - +
317A LYS* 3.6 10.1 - - - +
318A PHE 3.2 0.4 - - - -
319A ARG* 1.3 79.4 - - - +
321A GLU* 1.3 62.7 + - - +
323A ILE* 3.4 12.9 + - - +
324A SER* 3.3 20.6 + - - -
373A GLN* 3.6 34.5 - - - +
375A TYR* 4.1 7.1 + - + -
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Residues in contact with GLU 321 (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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293A LYS* 3.5 38.9 + - + +
317A LYS 3.3 9.2 + - - +
318A PHE* 3.0 33.6 + - + +
320A GLU* 1.3 79.7 - - - +
322A VAL* 1.3 58.9 + - - +
324A SER* 2.9 25.5 + - - +
325A ILE* 3.8 6.6 - - - +
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Residues in contact with VAL 322 (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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292A PHE* 4.1 11.2 - - + -
293A LYS* 4.8 9.2 - - + -
296A VAL* 3.8 31.1 - - + +
310A LEU* 4.1 12.1 - - + -
318A PHE* 2.9 52.9 + - + +
319A ARG 3.9 2.5 - - - +
321A GLU* 1.3 74.3 - - - +
323A ILE* 1.3 68.6 + - - +
325A ILE* 3.1 21.2 + - + +
326A GLY 3.6 5.0 + - - -
327A ILE* 3.6 16.9 - - + +
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Residues in contact with ILE 323 (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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70A LYS* 3.1 21.7 - - - -
78A ILE* 3.6 29.6 - - + -
310A LEU* 4.4 3.4 - - + -
319A ARG* 2.9 38.1 + - + +
320A GLU* 3.5 11.0 - - - +
321A GLU 3.3 0.4 - - - -
322A VAL* 1.3 78.1 - - - +
324A SER* 1.3 62.7 + - - +
325A ILE 3.1 1.7 + - - -
327A ILE* 3.2 29.8 + - + -
330A ILE* 3.8 30.7 - - + -
370A LEU* 4.6 11.7 - - + -
375A TYR* 4.0 19.5 - - + -
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Residues in contact with SER 324 (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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67A ARG* 3.1 43.2 + - - +
70A LYS* 3.8 13.4 - - - +
293A LYS* 5.4 0.5 - - - -
320A GLU 3.3 6.5 + - - -
321A GLU* 2.9 19.1 + - - +
322A VAL 3.2 0.4 - - - -
323A ILE* 1.3 77.3 - - - +
325A ILE* 1.3 60.8 + - - +
326A GLY 3.5 0.7 + - - -
375A TYR* 3.4 22.3 + - - -
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Residues in contact with ILE 325 (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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63A PHE* 3.9 24.0 - - + +
66A ALA* 3.4 26.8 - - + +
67A ARG* 3.7 40.6 - - + +
293A LYS* 3.4 39.0 - - + +
296A VAL* 3.4 34.4 - - + +
297A ALA* 4.0 6.0 - - + +
300A ARG* 3.8 6.9 - - - +
321A GLU 3.8 10.5 - - - +
322A VAL* 3.1 12.3 + - + +
323A ILE 3.1 0.2 + - - -
324A SER* 1.3 77.2 - - - +
326A GLY* 1.3 57.0 + - - +
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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