Contacts of the helix formed by residues 418 - 424 (chain A) in PDB entry 4GB1
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 PRO 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A MET* 3.6 19.7 - - + -
87A ASN* 4.8 9.4 - - - +
124A CYS* 3.5 24.0 - - + +
125A SER 3.4 27.1 - - - +
126A PRO* 4.1 4.0 - - + -
416A THR* 3.7 2.9 - - - +
417A LEU* 1.3 84.9 - - + +
419A VAL* 1.3 56.5 + - - +
420A GLU* 3.3 18.4 - - - +
421A LEU* 2.8 37.4 + - + +
423A SER* 3.1 11.5 + - - -
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Residues in contact with VAL 419 (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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86A ASN 5.1 3.6 + - - +
87A ASN* 5.5 0.4 - - - +
89A GLU* 3.6 36.3 - - + +
417A LEU 3.5 2.6 + - - -
418A PRO* 1.3 69.2 - - - +
420A GLU* 1.3 67.4 + - + +
421A LEU 2.9 6.1 + - - -
423A SER* 4.0 5.4 - - - -
424A GLY* 3.1 24.3 + - - +
425A LYS 3.2 26.0 - - - +
426A ASP* 4.6 2.7 - - - -
427A CYS 4.3 7.4 - - - +
428A LEU* 4.2 12.0 - - + +
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Residues in contact with GLU 420 (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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83A THR* 6.0 1.0 - - - +
84A TYR 4.8 1.6 - - - +
85A MET* 3.4 34.1 - - - +
86A ASN 4.3 6.0 + - - +
126A PRO* 3.8 28.9 - - + +
418A PRO* 3.1 18.1 - - - +
419A VAL* 1.3 80.8 + - + +
421A LEU* 1.3 58.9 + - - +
424A GLY 5.1 0.2 - - - -
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Residues in contact with LEU 421 (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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125A SER 3.6 21.1 - - - +
126A PRO 3.4 19.5 - - - +
127A ILE* 4.0 11.0 - - - +
128A GLU* 3.9 15.5 - - - +
129A CYS* 4.3 16.4 - - - +
417A LEU* 5.3 5.8 - - + -
418A PRO* 2.8 22.6 + - + +
420A GLU* 1.3 81.1 - - - +
423A SER* 1.3 61.0 + - - +
424A GLY 3.5 1.3 - - - -
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Residues in contact with SER 423 (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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417A LEU* 4.0 28.1 + - - -
418A PRO 3.1 14.0 + - - -
419A VAL* 4.0 5.4 + - - -
421A LEU* 1.3 77.6 - - - +
424A GLY* 1.3 61.1 + - - +
425A LYS* 3.0 28.5 + - - +
427A CYS 4.4 2.3 + - - -
429A VAL* 4.2 13.6 - - - +
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Residues in contact with GLY 424 (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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419A VAL* 3.1 13.5 + - - +
420A GLU 5.1 0.2 - - - -
421A LEU 3.5 1.8 - - - -
423A SER* 1.3 77.3 + - - +
425A LYS* 1.3 64.3 + - - +
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Residues in contact with LYS 425 (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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92A CYS* 3.9 16.0 - - - +
419A VAL* 3.2 30.0 - - - +
423A SER* 3.0 19.0 + - - +
424A GLY* 1.3 80.7 - - - +
426A ASP* 1.3 62.1 + - - +
427A CYS* 3.1 19.3 - - - +
429A VAL* 3.6 27.2 - - + +
458A GLY 4.2 12.7 + - - -
459A VAL* 4.9 3.2 - - - +
460A ASP* 3.9 26.1 + - - +
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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