Contacts of the helix formed by residues 405 - 411 (chain A) in PDB entry 5V5Z
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 SER 405 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A TYR* 3.8 1.7 - - - -
72A PHE* 3.5 25.8 - - - -
94A VAL* 5.6 1.1 - - - -
95A TYR 5.0 2.6 + - - -
96A LEU* 4.9 9.0 - - - +
97A GLY 5.6 2.4 + - - -
101A HIS* 4.4 3.5 + - - -
377A HIS 3.0 21.4 + - - -
379A ILE 5.2 0.2 - - - +
403A LEU* 4.3 4.0 - - - -
404A VAL* 1.3 84.5 - - - +
406A PRO* 1.3 56.5 - - - +
407A GLY 2.6 13.4 + - - -
408A TYR* 3.0 27.4 + - - +
409A ALA* 3.9 2.6 + - - +
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Residues in contact with PRO 406 (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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101A HIS* 3.4 19.9 - - + +
105A PHE* 3.9 16.4 - - + -
374A MET* 3.7 16.6 - - + -
377A HIS 5.1 0.4 - - - +
379A ILE* 4.3 8.1 - - + -
404A VAL* 3.8 15.7 - - + -
405A SER* 1.3 86.2 - - - +
407A GLY* 1.3 55.3 + - - +
408A TYR 3.6 0.2 - - - -
409A ALA* 3.8 2.8 + - + +
410A HIS* 2.9 37.1 + - + -
459A PRO 3.9 1.4 - - - +
461A LEU* 3.4 44.0 - - + +
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Residues in contact with GLY 407 (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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69A TYR* 3.5 21.3 - - - -
374A MET* 3.1 23.4 - - - +
405A SER* 2.6 9.1 + - - -
406A PRO* 1.3 73.0 - - - +
408A TYR* 1.3 65.1 + - - +
410A HIS* 2.8 20.4 + - - +
411A THR* 3.2 14.0 + - - -
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Residues in contact with TYR 408 (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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69A TYR* 3.2 28.8 - + + -
72A PHE* 4.0 24.7 - + + -
73A GLU* 2.7 34.0 + - + -
76A ARG* 3.1 14.8 + - - -
96A LEU* 3.5 40.6 - - + -
97A GLY 4.6 3.6 - - - -
405A SER* 3.0 14.6 + - - +
407A GLY* 1.3 76.2 - - - +
409A ALA* 1.3 66.3 + - + +
411A THR* 3.1 13.3 + - - +
412A SER* 3.5 24.4 + - - -
414A ARG* 2.7 34.2 + - - -
415A TYR* 4.9 2.5 - + - -
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Residues in contact with ALA 409 (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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97A GLY* 4.5 16.4 - - - +
101A HIS* 4.6 7.2 - - - +
405A SER 3.9 2.1 + - - +
406A PRO 3.8 4.9 + - - +
407A GLY 3.3 0.4 - - - -
408A TYR* 1.3 84.0 - - + +
410A HIS* 1.3 61.1 + - - +
411A THR 3.3 0.5 + - - -
412A SER* 3.7 5.4 + - - -
415A TYR* 3.8 35.2 - - + +
416A PHE* 3.6 16.6 - - - -
459A PRO* 3.8 20.4 - - + +
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Residues in contact with HIS 410 (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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370A LEU 4.0 0.9 + - - -
371A ARG* 3.0 51.3 + - + +
374A MET* 3.9 19.2 - - + +
406A PRO 2.9 25.6 + - - -
407A GLY* 2.8 16.7 + - - +
409A ALA* 1.3 77.8 - - - +
411A THR* 1.3 56.7 + - - +
412A SER 3.7 0.4 - - - -
416A PHE* 3.7 8.7 - + - -
459A PRO 3.4 12.1 - - - -
460A TYR* 3.1 28.6 - + - -
461A LEU 2.9 25.7 + - - -
462A PRO* 3.5 31.2 - - + -
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Residues in contact with THR 411 (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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69A TYR* 4.9 12.8 - - - +
371A ARG* 3.9 14.1 - - - +
372A MET* 4.3 24.9 - - + +
407A GLY 3.2 13.2 + - - -
408A TYR* 3.1 8.7 + - - +
410A HIS* 1.3 83.5 - - - +
412A SER* 1.3 54.1 + - - +
419A PRO* 3.7 28.0 - - + +
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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