Contacts of the helix formed by residues 316 - 324 (chain A) in PDB entry 4U7C
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 ASN 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ASN 5.5 2.4 + - - -
99A LEU* 6.1 0.6 - - - +
103A ILE* 4.0 8.7 - - - -
314A ALA* 3.2 1.5 - - - +
315A PRO* 1.3 82.2 - - - +
317A THR* 1.3 59.6 + - - +
318A MET* 3.4 10.7 + - - +
319A LEU* 3.0 37.8 + - - +
320A ALA* 3.0 28.4 + - - +
401A GLY 2.8 27.0 + - - -
402A LEU* 3.9 4.7 - - - +
403A GLY 3.7 19.0 - - - +
404A SER 3.3 14.8 - - - +
405A THR* 3.8 4.9 - - + +
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Residues in contact with THR 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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103A ILE* 3.9 13.9 - - + +
193A MET* 5.6 1.8 - - + -
201A TYR* 3.5 28.6 - - + -
316A ASN* 1.3 71.6 - - - +
318A MET* 1.3 62.2 + - - +
320A ALA* 3.3 0.7 + - - +
321A LYS* 2.9 31.9 + - - +
403A GLY* 4.6 0.3 - - - -
404A SER* 2.6 45.5 + - - +
405A THR* 5.6 0.2 - - - -
407A LEU* 3.7 29.6 - - + -
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Residues in contact with MET 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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201A TYR* 5.7 0.2 - - - -
316A ASN* 3.4 5.3 + - - +
317A THR* 1.3 81.2 + - - +
319A LEU* 1.3 76.1 + - + +
321A LYS* 3.3 5.9 + - - +
322A VAL* 3.0 34.5 + - - +
346A ILE* 5.6 1.1 - - + -
349A LEU* 5.6 4.9 - - - -
354A VAL* 3.5 35.0 - - + -
355A SER* 5.4 4.0 - - - +
394A TYR* 5.7 0.2 - - - +
398A ILE* 3.9 26.9 - - + +
401A GLY* 3.7 25.1 - - - +
402A LEU 3.2 29.8 - - - +
403A GLY* 4.5 5.6 - - - -
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Residues in contact with LEU 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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314A ALA* 3.5 14.8 - - + -
315A PRO* 4.1 21.5 - - + -
316A ASN* 3.0 36.6 + - - +
318A MET* 1.3 93.0 - - + +
320A ALA* 1.3 58.0 + - - +
322A VAL* 3.1 7.7 + - + +
323A CYS* 2.9 30.7 + - - -
335A ILE* 4.0 20.0 - - + +
342A VAL* 3.9 25.4 - - + +
345A PHE* 4.4 11.7 - - + -
346A ILE* 4.6 10.1 - - + -
349A LEU* 6.0 2.0 - - + -
401A GLY 3.7 9.4 - - - +
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Residues in contact with ALA 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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103A ILE* 3.8 33.0 - - + +
105A HIS* 3.8 10.9 - - + +
201A TYR* 4.8 0.4 - - + -
312A GLY* 3.6 15.1 - - - +
314A ALA* 3.4 9.5 - - + +
316A ASN 3.0 17.6 + - - +
317A THR 3.6 4.5 - - - +
319A LEU* 1.3 74.0 - - - +
321A LYS* 1.3 57.7 + - - +
323A CYS* 3.2 7.4 + - - +
324A SER* 2.9 28.1 + - - -
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Residues in contact with LYS 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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105A HIS* 3.5 33.5 - - + +
107A ASP* 4.3 4.0 + - - -
199A GLU* 3.8 11.3 + - - -
201A TYR* 3.2 28.9 - - + +
317A THR 2.9 12.2 + - - +
318A MET* 3.6 6.5 - - - +
319A LEU 3.2 0.2 - - - -
320A ALA* 1.3 75.4 - - - +
322A VAL* 1.3 65.1 + - + +
324A SER* 3.4 14.2 + - - -
325A ASP* 3.9 15.6 + - - +
353A LYS 5.3 5.6 - - - +
355A SER* 4.4 24.2 - - - +
13C G 3.1 32.0 + - - +
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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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318A MET* 3.0 31.7 + - - +
319A LEU* 3.1 6.9 + - + +
321A LYS* 1.3 78.6 - - + +
323A CYS* 1.3 63.5 + - - +
325A ASP* 3.4 16.0 + - - +
326A LYS* 3.9 5.2 + - - +
345A PHE* 3.9 18.5 - - + -
349A LEU* 3.7 35.7 - - + -
353A LYS* 4.0 28.9 - - + +
354A VAL* 4.3 9.2 - - + -
355A SER 5.3 1.3 - - - +
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Residues in contact with CYS 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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311A ALA 4.4 0.7 - - - +
312A GLY* 3.5 15.3 - - - -
313A ILE 4.0 13.0 - - - +
314A ALA* 4.3 0.2 - - - -
319A LEU 2.9 18.6 + - - -
320A ALA 3.3 8.3 - - - +
322A VAL* 1.3 72.2 - - - +
324A SER* 1.3 54.1 + - - +
325A ASP 2.7 16.6 + - - -
326A LYS* 2.8 21.1 + - - +
327A ASN 4.2 2.3 + - - -
332A GLN 5.6 0.2 - - - -
333A TYR* 3.9 24.4 - - + +
335A ILE* 3.5 35.7 - - - -
345A PHE* 4.4 8.5 - - - -
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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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105A HIS* 2.9 50.0 + - - -
107A ASP* 4.2 7.6 - - - +
310A SER* 3.4 24.6 - - - -
311A ALA* 3.5 17.4 - - - +
312A GLY* 3.5 2.8 - - - -
320A ALA 2.9 8.8 + - - -
321A LYS 3.4 4.2 + - - -
322A VAL 3.5 0.2 - - - -
323A CYS* 1.3 73.1 - - - +
325A ASP* 1.3 71.7 + - - +
326A LYS 3.6 0.4 + - - -
327A ASN 4.8 1.5 + - - -
328A LYS* 3.8 6.2 + - - +
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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