Contacts of the helix formed by residues 405 - 416 (chain A) in PDB entry 1GXD
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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387A ASP* 4.2 5.7 + - - -
389A GLY 3.4 24.5 + - - -
390A ALA* 4.0 3.0 - - - -
403A ARG 3.4 2.1 + - - -
404A LEU* 1.3 70.9 - - - +
406A GLN* 1.3 59.0 + - - +
407A ASP* 3.0 21.8 + - - +
408A ASP* 2.4 46.5 + - - -
409A ILE 2.8 4.5 + - - -
432A LEU* 2.7 9.5 - - - +
435A VAL* 6.0 0.9 - - - +
462A ARG* 5.8 0.7 - - - -
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Residues in contact with GLN 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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405A SER* 1.3 69.6 + - - +
407A ASP* 1.3 68.7 + - - +
409A ILE* 2.7 8.9 + - - +
410A LYS* 2.5 48.7 + - + +
431A THR* 3.7 15.9 - - - +
432A LEU* 2.3 63.7 - - + +
433A GLY 5.3 2.5 - - - +
434A PRO 4.3 16.4 + - - +
435A VAL* 4.9 20.4 - - + -
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Residues in contact with ASP 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A SER* 2.8 34.3 + - - -
387A ASP* 3.7 21.1 - - - +
390A ALA* 3.4 7.5 - - + +
405A SER* 3.0 12.8 + - - +
406A GLN* 1.3 78.2 - - - +
408A ASP* 1.3 60.7 + - - +
410A LYS* 3.3 25.1 + - - +
411A GLY* 3.0 18.7 + - - -
435A VAL* 5.5 3.9 - - + +
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Residues in contact with ASP 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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122A TRP* 4.1 9.4 - - + -
382A LEU* 4.7 4.2 - - - +
390A ALA* 3.6 8.7 - - - +
391A LEU* 3.0 33.7 + - - +
392A MET* 3.4 17.0 + - - +
404A LEU* 3.3 28.0 - - + +
405A SER* 2.4 40.4 + - - +
407A ASP* 1.3 67.0 - - - +
409A ILE* 1.3 69.0 + - - +
410A LYS 2.7 3.1 + - - -
411A GLY* 2.8 13.5 + - - -
412A ILE* 2.9 16.5 + - - +
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Residues in contact with ILE 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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125A VAL* 3.6 27.1 - - + -
404A LEU* 4.0 15.9 - - + +
405A SER 2.8 1.7 + - - +
406A GLN* 2.7 10.4 + - - +
408A ASP* 1.3 71.2 - - - +
410A LYS* 1.3 65.9 + - - +
412A ILE* 3.7 7.9 - - - -
413A GLN* 2.9 58.1 + - + +
431A THR* 5.9 2.7 - - + -
432A LEU* 1.9 72.2 - - + +
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Residues in contact with LYS 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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406A GLN* 2.5 38.5 + - + +
407A ASP* 3.3 31.0 + - - +
408A ASP 2.7 1.2 + - - -
409A ILE* 1.3 75.4 - - - +
411A GLY* 1.3 66.5 + - - +
413A GLN* 3.7 3.1 - - - +
414A GLU* 2.8 32.8 + - + +
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Residues in contact with GLY 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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382A LEU* 3.8 20.8 - - - +
407A ASP 3.0 8.3 + - - -
408A ASP* 2.8 10.4 + - - -
410A LYS* 1.3 76.4 - - - +
412A ILE* 1.3 59.1 + - - -
414A GLU* 3.3 24.1 - - - +
415A LEU* 3.6 16.1 + - - +
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Residues in contact with ILE 412 (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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122A TRP* 3.8 24.9 - - + -
125A VAL* 3.7 19.1 - - + -
126A THR* 3.8 18.2 - - + -
128A LEU* 4.6 1.3 - - + -
377A GLY* 5.2 0.2 - - - -
380A MET* 3.8 34.5 - - + -
382A LEU* 3.8 26.7 - - + +
408A ASP 2.9 11.3 + - - +
409A ILE* 3.2 20.0 - - - +
411A GLY* 1.3 72.8 - - - +
413A GLN* 1.3 65.8 + - + +
414A GLU 3.2 0.2 - - - -
415A LEU* 3.2 4.3 + - + +
416A TYR* 3.0 36.8 + - + +
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Residues in contact with GLN 413 (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 VAL* 3.3 27.3 + - - +
126A THR* 5.2 0.2 - - - -
409A ILE* 2.9 48.9 + - + +
410A LYS* 3.8 2.5 - - - +
412A ILE* 1.3 76.8 - - + +
414A GLU* 1.3 62.4 + - - +
416A TYR 2.1 30.2 - - - +
417A GLY 3.6 7.9 - - - +
418A ALA* 3.3 30.0 + - + +
419A SER* 5.4 0.4 + - - -
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Residues in contact with GLU 414 (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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410A LYS* 2.8 28.2 + - + +
411A GLY* 3.3 17.5 + - - +
413A GLN* 1.3 78.7 - - - +
415A LEU* 1.3 61.0 + - + +
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Residues in contact with LEU 415 (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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88A PRO* 3.1 31.9 - - + +
89A LYS* 3.6 25.3 - - + +
380A MET 4.1 13.7 - - - +
381A GLY 4.5 11.4 - - - +
382A LEU* 4.5 12.3 - - + -
411A GLY 3.7 16.2 - - - +
412A ILE* 3.2 4.3 + - + +
413A GLN 3.1 0.4 - - - -
414A GLU* 1.3 84.2 - - + +
416A TYR* 1.3 81.5 + - + +
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Residues in contact with TYR 416 (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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89A LYS* 3.5 7.2 - - + -
90A TRP* 2.6 61.7 + + + -
92A LYS 4.4 1.3 - - - -
93A ASN* 4.1 9.4 - - - -
126A THR* 4.4 5.2 - - - -
127A PRO* 4.5 2.9 - - + -
128A LEU* 3.6 36.3 - - + -
380A MET* 2.7 39.8 + - + -
412A ILE* 3.0 25.1 + - + +
413A GLN 2.1 30.5 - - - +
415A LEU* 1.3 89.7 - - + +
417A GLY* 1.3 68.1 + - - +
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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