Contacts of the helix formed by residues 328 - 334 (chain A) in PDB entry 5IVI
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 HIS 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A ASN* 4.7 9.7 + - - -
255A GLN* 4.9 17.3 + - + +
315A VAL* 3.6 26.4 - - + +
327A LYS* 1.3 76.7 - - - +
329A PRO* 1.3 78.2 - - + +
330A ARG* 3.2 4.9 - - + +
331A GLU* 2.9 27.4 + - + +
332A MET 3.0 9.2 + - - -
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Residues in contact with PRO 329 (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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226A TYR* 4.8 6.7 - - + +
229A LEU* 4.3 6.4 - - + +
247A ALA* 3.6 44.2 - - + +
248A ILE* 4.6 9.4 - - + +
253A ASN* 3.9 18.6 - - + +
315A VAL* 4.8 3.6 - - + -
325A LEU* 6.3 1.8 - - + -
327A LYS 3.6 2.4 - - - +
328A HIS* 1.3 93.0 - - + +
330A ARG* 1.3 60.0 + - + +
332A MET* 3.1 12.2 + - + +
333A VAL* 2.9 34.2 + - + +
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Residues in contact with ARG 330 (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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248A ILE* 4.1 22.7 - - + -
328A HIS* 3.2 3.7 - - + +
329A PRO* 1.3 81.4 - - + +
331A GLU* 1.3 78.8 + - + +
333A VAL* 3.4 9.9 + - - +
334A LYS* 3.7 14.9 + - - +
379A GLU* 5.0 2.5 - - - -
427A ARG* 3.8 22.2 - - - +
431A LEU* 3.4 41.1 - - + +
568A ASP 3.0 25.7 + - - -
569A LEU* 3.2 21.4 + - - +
570A PHE* 2.9 33.0 + - - -
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Residues in contact with GLU 331 (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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327A LYS* 3.9 29.5 - - + +
328A HIS* 2.9 23.1 + - + +
330A ARG* 1.3 95.2 + - - +
332A MET* 1.3 64.3 + - - +
334A LYS* 3.2 52.9 + - + +
335A THR* 4.1 5.4 + - - +
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Residues in contact with MET 332 (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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229A LEU* 3.8 37.2 - - + +
230A THR* 3.8 8.7 - - - -
231A GLU 5.2 0.7 - - - +
324A VAL 3.4 22.0 - - - +
325A LEU* 3.7 28.0 - - + -
326A PRO* 3.9 11.7 - - + -
327A LYS* 3.4 29.8 - - + +
328A HIS 3.0 15.2 + - - +
329A PRO* 3.1 12.1 + - + +
331A GLU* 1.3 75.4 - - - +
333A VAL* 1.3 65.2 + - - +
335A THR* 3.2 10.7 + - - -
336A ALA* 3.1 22.0 + - - +
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Residues in contact with VAL 333 (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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225A HIS* 4.4 5.4 - - + -
229A LEU* 3.8 20.6 - - + -
248A ILE* 4.5 3.8 - - + -
329A PRO 2.9 23.0 + - - +
330A ARG* 3.6 11.2 - - - +
331A GLU 3.2 0.4 - - - -
332A MET* 1.3 78.0 - - - +
334A LYS* 1.3 59.1 + - - +
335A THR 3.1 0.9 + - - -
336A ALA* 3.3 2.2 + - - -
339A ASN* 2.6 43.5 + - - +
428A LEU* 4.0 21.8 - - + -
431A LEU* 3.7 27.6 - - + +
432A ARG* 4.1 15.5 - - - +
435A HIS* 3.9 0.7 - - - +
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Residues in contact with LYS 334 (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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330A ARG* 3.8 15.7 - - - +
331A GLU* 3.2 44.8 + - - +
332A MET 3.1 1.2 - - - -
333A VAL* 1.3 76.7 - - - +
335A THR* 1.3 65.3 + - + +
431A LEU* 4.6 12.8 - - + -
435A HIS* 3.5 52.9 - - + +
568A ASP 5.6 3.6 + - - -
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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