Contacts of the helix formed by residues 455 - 461 (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 ASN 455 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A MET* 5.3 2.7 - - + -
454A ILE* 1.3 78.7 - - - +
456A PRO* 1.3 69.6 - - + +
457A TYR* 3.2 34.1 + - - +
458A ARG* 2.9 32.3 + - - +
459A ILE 4.0 1.0 + - - -
472A THR 3.4 21.4 + - - +
473A ASP* 4.1 10.9 + - - +
475A LEU* 4.8 5.8 - - + -
476A THR* 2.7 31.6 + - - +
481A ASN* 3.7 9.6 - - + +
483A LEU* 4.0 7.2 - - - +
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Residues in contact with PRO 456 (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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13A TRP* 3.7 26.7 - - + -
100A PHE* 3.7 28.3 - - + -
146A ASP 4.9 2.9 - - - +
147A MET* 3.5 31.2 - - - -
455A ASN* 1.3 86.3 - - + +
457A TYR* 1.3 61.3 + - - +
458A ARG 3.1 0.4 - - - -
459A ILE* 3.0 8.3 + - + +
460A MET 3.0 18.4 + - - -
481A ASN* 3.5 21.5 - - + +
482A GLN* 4.9 0.7 - - + +
483A LEU* 3.9 13.4 - - + -
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Residues in contact with TYR 457 (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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100A PHE* 4.9 2.5 - + - -
135A GLY* 3.6 22.0 + - - -
136A GLY* 3.7 11.7 + - - -
140A ILE* 4.7 11.2 - - + +
147A MET* 3.7 24.9 - - + -
148A TYR* 3.8 14.6 + - - -
217A GLU* 4.8 2.0 + - - -
354A PHE* 4.7 1.8 - + + -
455A ASN* 3.0 22.0 + - - +
456A PRO* 1.3 78.1 - - - +
458A ARG* 1.3 61.3 + - - +
460A MET* 3.3 34.9 + - + +
461A ARG* 3.0 28.7 + - - +
472A THR* 3.3 28.9 - - + +
475A LEU* 3.8 14.8 - - + -
601A DPF 3.3 26.2 - - + -
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Residues in contact with ARG 458 (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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449A ASP* 4.7 5.9 + - - -
450A SER 3.7 14.6 + - - -
451A GLU* 3.3 32.1 + - - +
453A LEU 5.3 1.0 + - - -
454A ILE* 3.5 39.2 - - + +
455A ASN* 2.9 21.3 + - - +
457A TYR* 1.3 79.5 - - - +
459A ILE* 1.3 60.3 + - + +
461A ARG* 3.5 24.2 - - - +
462A SER* 3.3 1.9 + - - -
463A GLY* 2.8 57.5 + - - +
464A ARG* 3.9 10.8 + - + +
466A VAL 3.9 8.5 + - - -
468A GLY 5.4 0.6 + - - -
472A THR* 5.0 0.4 + - - -
473A ASP* 3.4 30.3 + - - +
476A THR* 5.9 0.6 + - - -
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Residues in contact with ILE 459 (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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5A VAL* 3.6 30.2 - - + +
9A GLU* 3.8 22.1 - - + +
13A TRP* 5.1 7.6 - - + -
101A ILE* 4.1 15.5 - - + -
454A ILE* 4.1 13.2 - - + -
455A ASN 4.7 0.4 - - - +
456A PRO* 3.0 8.7 + - + +
458A ARG* 1.3 80.1 - - + +
460A MET* 1.3 66.4 + - - +
462A SER* 3.0 14.9 + - - +
464A ARG* 3.1 38.4 - - + +
483A LEU* 3.8 25.1 - - + -
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Residues in contact with MET 460 (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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5A VAL* 4.1 17.7 + - - +
100A PHE* 3.4 50.3 - - + +
101A ILE* 4.6 1.3 - - - +
140A ILE* 4.1 14.6 - - + -
354A PHE* 3.4 34.5 - - + -
456A PRO 3.0 6.5 + - - +
457A TYR* 3.5 31.0 - - + +
459A ILE* 1.3 78.7 - - - +
461A ARG* 1.3 57.0 + - + +
462A SER* 3.6 0.9 + - - -
601A DPF 4.6 2.2 - - + -
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Residues in contact with ARG 461 (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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353A LEU 4.3 5.7 + - - -
354A PHE* 3.7 55.4 - - + +
356A THR* 5.9 1.5 - - - -
357A SER* 3.3 24.6 + - - +
457A TYR 3.0 15.8 + - - +
458A ARG* 3.5 44.3 - - - +
460A MET* 1.3 75.5 - - - +
462A SER* 1.3 70.8 + - - +
463A GLY* 3.3 19.8 + - - +
466A VAL* 4.6 10.7 + - - +
468A GLY 5.5 0.4 + - - -
470A SER* 2.9 26.9 + - - -
471A HIS 4.4 1.8 + - - -
472A THR* 4.6 1.0 + - - -
473A ASP* 2.7 36.2 + - - -
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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