Contacts of the helix formed by residues 405 - 417 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387B ASP* 5.3 2.5 - - - -
389B GLY 3.5 24.5 - - - -
390B ALA* 3.1 16.2 - - - +
391B LEU 5.3 0.4 - - - +
403B ARG 3.0 5.3 + - - -
404B LEU* 1.3 77.2 - - - +
406B GLN* 1.3 62.2 + - - +
407B ASP* 3.4 5.0 + - - +
408B ASP* 2.8 34.5 + - - +
409B ILE* 3.1 13.8 + - - +
434B PRO* 3.6 14.1 - - - -
436B THR* 5.4 3.1 - - - -
462B ARG* 4.2 6.7 - - - -
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Residues in contact with GLN 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405B SER* 1.3 72.1 - - - +
407B ASP* 1.3 60.2 + - - +
409B ILE* 2.8 9.5 + - - +
410B LYS* 2.8 46.3 + - + +
413B GLN* 5.4 2.4 - - - +
431B THR* 3.3 16.2 + - + +
432B LEU 1.9 40.2 + - - +
433B GLY* 3.2 7.3 + - - +
434B PRO 2.7 27.3 + - - +
435B VAL* 4.8 7.0 - - + -
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Residues in contact with ASP 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B SER* 2.7 34.4 + - - -
387B ASP* 3.8 23.7 + - - +
390B ALA* 3.2 11.2 - - + +
405B SER* 3.2 9.4 - - - +
406B GLN* 1.3 78.7 - - - +
408B ASP* 1.3 60.4 + - - +
410B LYS* 4.2 15.1 + - - +
411B GLY* 3.4 16.9 + - - -
434B PRO 4.4 0.2 + - - -
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Residues in contact with ASP 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B TRP* 3.9 10.2 - - + -
382B LEU* 4.4 3.7 - - - +
390B ALA* 3.6 5.4 - - - +
391B LEU* 2.8 31.4 + - - +
392B MET* 3.1 31.8 + - - +
404B LEU* 3.4 20.6 - - + +
405B SER* 2.8 28.7 + - - +
406B GLN 3.0 0.8 - - - -
407B ASP* 1.3 77.5 - - - +
409B ILE* 1.3 53.5 + - - +
411B GLY* 3.2 2.4 + - - -
412B ILE* 2.8 37.9 + - - +
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Residues in contact with ILE 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B VAL* 4.0 22.4 - - + -
404B LEU* 4.0 20.0 - - + +
405B SER 3.1 15.5 - - - +
406B GLN* 2.8 9.9 + - - +
408B ASP* 1.3 72.2 - - - +
410B LYS* 1.3 57.3 + - - +
411B GLY 3.0 0.2 + - - -
412B ILE* 3.2 6.5 - - - +
413B GLN* 2.6 73.1 + - + +
432B LEU* 3.6 19.5 - - + +
433B GLY* 3.6 30.5 - - - +
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Residues in contact with LYS 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B GLN* 2.8 32.1 + - + +
407B ASP* 4.2 15.1 + - - +
409B ILE* 1.3 71.5 - - - +
411B GLY* 1.3 71.0 - - - +
413B GLN* 3.8 8.7 - - - +
414B GLU* 3.0 37.4 + - - +
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Residues in contact with GLY 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B LEU* 3.8 16.0 - - - +
407B ASP 3.4 10.4 + - - -
408B ASP 3.2 6.8 + - - -
409B ILE 3.0 1.8 - - - -
410B LYS* 1.3 87.7 - - - +
412B ILE* 1.3 60.9 + - - -
414B GLU* 2.8 19.1 + - - +
415B LEU* 3.9 4.9 + - - +
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Residues in contact with ILE 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B TRP* 3.6 33.4 - - + -
125B VAL* 4.0 15.0 - - + -
126B THR* 3.9 16.8 - - + -
128B LEU* 4.6 4.7 - - + -
380B MET* 3.9 19.5 - - + -
382B LEU* 3.6 19.7 - - + +
408B ASP 2.8 18.6 + - - +
409B ILE* 3.2 16.6 - - - +
411B GLY* 1.3 70.9 - - - -
413B GLN* 1.3 65.9 + - + +
414B GLU 3.3 0.3 + - - -
415B LEU* 3.4 9.6 + - + +
416B TYR* 3.4 38.7 + - + +
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Residues in contact with GLN 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B VAL 3.6 11.2 + - - +
406B GLN* 5.4 2.3 - - - +
409B ILE* 2.6 50.2 + - + +
410B LYS* 3.9 6.2 - - - +
412B ILE* 1.3 70.8 - - + +
414B GLU* 1.3 61.0 + - - +
415B LEU 3.1 5.4 - - - -
416B TYR 3.4 0.4 + - - -
417B GLY* 3.1 25.4 + - - +
418B ALA* 3.0 51.2 + - - +
432B LEU* 3.9 14.6 - - - +
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Residues in contact with GLU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B LYS* 3.0 28.5 + - - +
411B GLY* 2.8 16.4 + - - +
413B GLN* 1.3 76.6 - - - +
415B LEU* 1.3 62.5 + - + +
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B PRO* 3.4 31.2 - - + +
89B LYS* 2.8 41.2 - - + +
380B MET 4.1 9.4 - - - +
381B GLY 4.4 8.5 - - - +
382B LEU* 4.2 25.1 - - + -
411B GLY 4.5 4.7 - - - +
412B ILE* 3.4 1.7 + - + +
413B GLN 3.1 0.4 - - - -
414B GLU* 1.3 86.0 - - + +
416B TYR* 1.3 83.7 + - + +
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Residues in contact with TYR 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B LYS* 3.3 29.9 - - + +
90B TRP* 3.2 33.7 + - + -
92B LYS 4.8 0.4 - - - -
93B ASN* 4.3 8.3 + - - +
126B THR* 4.1 13.2 - - + -
127B PRO* 3.6 21.9 - - + +
128B LEU* 3.6 29.8 - - + -
380B MET* 2.5 33.5 + - + -
412B ILE* 3.4 38.0 + - + +
413B GLN 3.4 0.8 + - - -
415B LEU* 1.3 92.6 - - + +
417B GLY* 1.3 60.9 + - - +
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Residues in contact with GLY 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B THR* 3.1 31.5 - - - +
127B PRO* 3.4 4.0 - - - +
413B GLN* 3.1 18.1 + - - -
416B TYR* 1.3 77.1 - - - +
418B ALA* 1.3 59.5 + - - -
419B SER 3.4 2.9 - - - -
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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