Contacts of the helix formed by residues 403 - 417 (chain A) in PDB entry 1GC5
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 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A TYR* 4.9 10.9 + - - -
355A GLY* 3.5 29.7 - - - +
401A PRO 3.6 2.2 + - - -
402A THR* 1.3 71.4 - - - +
404A GLU* 1.3 61.1 + - - +
405A ARG* 3.2 10.2 + - - +
406A ALA* 2.6 45.8 + - + +
407A ILE* 3.4 12.6 + - - +
437A THR 2.7 21.8 + - - +
438A LYS* 4.7 0.4 - - - +
439A ILE* 3.9 18.3 - - + +
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Residues in contact with GLU 404 (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 LEU* 3.9 35.0 - - + +
9A ILE* 4.0 15.1 - - + +
402A THR 2.8 10.3 + - - +
403A ASN* 1.3 73.4 + - - +
405A ARG* 1.3 63.4 + - - +
407A ILE* 3.1 20.2 + - + +
408A VAL* 3.1 14.0 + - + +
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Residues in contact with ARG 405 (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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356A TYR* 5.9 1.6 - - - -
403A ASN* 3.2 9.2 + - - +
404A GLU* 1.3 75.1 - - - +
406A ALA* 1.3 61.4 + - - +
408A VAL* 3.2 11.6 + - + +
409A LEU* 3.0 58.6 + - + +
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Residues in contact with ALA 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A GLY* 3.1 30.1 - - - +
356A TYR* 4.3 4.0 - - + -
403A ASN* 2.6 22.6 + - - +
405A ARG* 1.3 74.2 - - - +
407A ILE* 1.3 61.5 + - - +
409A LEU* 3.3 12.4 + - - +
410A GLU 3.2 8.5 + - - -
434A PHE* 3.1 28.4 - - + -
436A PRO* 3.6 15.5 - - + -
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Residues in contact with ILE 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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5A LEU* 3.5 20.4 - - + -
8A ARG* 3.7 28.5 + - + +
9A ILE* 3.4 35.9 - - + -
12A TRP* 4.1 20.4 - - + +
402A THR* 4.3 17.3 - - + +
403A ASN 3.7 13.0 - - - +
404A GLU* 3.1 15.3 + - - +
406A ALA* 1.3 76.2 - - - +
408A VAL* 1.3 65.0 + - - +
410A GLU* 3.1 21.2 + - - +
411A GLU* 3.9 5.7 + - - +
436A PRO* 4.2 11.0 - - + -
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Residues in contact with VAL 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.3 33.7 - - + -
404A GLU* 3.1 8.8 + - + +
405A ARG* 3.2 14.1 + - + +
407A ILE* 1.3 78.8 - - - +
409A LEU* 1.3 63.3 + - + +
411A GLU* 3.2 40.3 + - - +
412A GLU* 4.2 9.7 + - - +
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Residues in contact with LEU 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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330A ILE* 4.5 31.6 - - + +
356A TYR* 4.5 16.8 - - + -
405A ARG* 3.0 53.9 + - + +
406A ALA* 3.4 17.3 - - - +
408A VAL* 1.3 78.2 - - + +
410A GLU* 1.3 63.4 + - - +
412A GLU* 3.2 37.6 + - - +
413A LEU* 3.5 12.7 + - - +
434A PHE* 4.7 5.4 - - + -
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Residues in contact with GLU 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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8A ARG* 4.2 7.6 + - - +
11A LEU* 5.3 0.3 - - - +
12A TRP* 3.1 36.2 + - - -
406A ALA 3.2 4.6 + - - -
407A ILE* 3.1 13.8 + - - +
409A LEU* 1.3 78.2 - - - +
411A GLU* 1.3 63.9 + - - +
413A LEU* 2.9 13.2 + - + +
414A GLU* 2.8 33.6 + - - +
419A GLU* 2.5 35.3 - - - +
422A ASN* 3.6 10.0 - - - +
423A GLY 3.1 15.1 + - - -
434A PHE* 3.9 22.6 - - + -
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Residues in contact with GLU 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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3A GLU 4.3 3.0 - - - +
5A LEU* 5.3 5.4 + - - +
8A ARG* 3.4 43.6 + - - +
407A ILE 4.2 1.1 - - - +
408A VAL* 3.3 34.8 - - - +
409A LEU 3.2 0.2 - - - -
410A GLU* 1.3 77.7 - - - +
412A GLU* 1.3 60.4 + - + +
414A GLU* 3.2 27.9 - - - +
415A LYS* 3.2 10.6 + - - +
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Residues in contact with GLU 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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330A ILE* 5.3 1.9 - - - +
331A PHE* 3.5 19.8 - - + -
408A VAL* 4.3 12.2 - - - +
409A LEU* 3.7 33.4 - - - +
410A GLU 3.1 0.8 - - - -
411A GLU* 1.3 73.7 - - + +
413A LEU* 1.3 65.0 + - - +
414A GLU 3.1 1.1 - - - -
415A LYS* 2.8 44.6 + - - +
416A GLU* 3.1 7.8 + - - +
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Residues in contact with LEU 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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330A ILE* 4.4 14.4 - - + -
331A PHE* 3.9 20.9 - - + -
334A ILE* 4.2 22.7 - - + -
358A LEU* 5.0 3.4 - - + -
409A LEU 3.5 11.6 + - - +
410A GLU* 2.9 10.6 + - + +
412A GLU* 1.3 77.3 - - - +
414A GLU* 1.3 56.3 + - - +
416A GLU 3.1 0.3 + - - -
417A PHE* 2.7 44.7 + - + +
419A GLU* 4.8 3.6 - - - +
425A ILE* 4.4 21.7 - - + +
432A LEU* 5.6 0.2 - - + -
434A PHE* 3.4 49.4 - - + -
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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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8A ARG* 2.9 39.4 + - - -
410A GLU* 2.8 25.2 + - - +
411A GLU* 3.2 14.7 - - - +
413A LEU* 1.3 78.6 - - - +
415A LYS* 1.3 58.0 + - - +
417A PHE 3.1 18.7 - - - +
419A GLU* 3.3 37.9 + - + +
422A ASN* 4.6 3.8 - - - +
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Residues in contact with LYS 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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331A PHE* 3.8 7.5 - - - -
411A GLU 3.2 8.0 + - - +
412A GLU* 2.8 43.4 + - - +
413A LEU 3.3 0.4 - - - -
414A GLU* 1.3 79.8 - - - +
416A GLU* 1.3 95.6 + - - +
417A PHE 4.6 0.4 - - - -
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A PHE* 3.3 29.9 - - + -
412A GLU 3.3 7.9 - - - +
413A LEU 3.1 2.5 + - - +
415A LYS* 1.3 120.3 - - - +
417A PHE* 1.3 74.1 + - + +
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Residues in contact with PHE 417 (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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331A PHE* 3.4 35.4 - + - -
334A ILE* 4.0 29.6 - - + -
413A LEU* 2.7 31.1 + - + +
414A GLU 3.1 19.1 - - - +
415A LYS 4.6 0.3 - - - -
416A GLU* 1.3 86.7 - - + +
418A THR* 1.3 63.0 + - - +
419A GLU 3.4 4.3 + - - -
425A ILE* 3.6 29.8 - - + -
427A MET* 3.7 28.5 - - + -
432A LEU* 4.8 0.9 - - + -
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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