Contacts of the helix formed by residues 445 - 459 (chain A) in PDB entry 3G0H
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 445 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A LEU* 4.8 3.1 - - - +
314A CYS 4.0 3.3 + - - -
315A SER* 5.5 0.4 - - - +
443A VAL* 3.3 9.8 - - - +
444A ASP* 1.3 90.3 + - - +
446A LYS* 1.3 60.1 + - - +
447A HIS* 3.1 10.5 + - - +
448A SER* 2.8 21.8 + - - -
449A MET* 3.1 20.6 + - - +
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Residues in contact with LYS 446 (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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445A SER* 1.3 73.5 - - - +
447A HIS* 1.3 64.5 + - - +
449A MET* 3.2 10.1 + - + +
450A ASN* 2.9 32.6 + - - +
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Residues in contact with HIS 447 (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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416A GLY 5.0 9.2 + - - -
445A SER* 3.1 7.5 + - - +
446A LYS* 1.3 78.9 - - - +
448A SER* 1.3 63.7 + - - +
450A ASN* 3.0 25.2 + - + +
451A ILE* 3.2 38.2 + - + +
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Residues in contact with SER 448 (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 LEU* 3.2 23.5 - - - +
442A MET 5.7 0.2 - - - -
443A VAL* 4.1 3.4 - - - -
444A ASP* 3.0 38.3 + - - -
445A SER* 2.8 14.4 + - - -
447A HIS* 1.3 79.5 + - - +
449A MET* 1.3 62.0 + - - +
451A ILE* 3.1 24.7 + - - +
452A LEU 3.2 9.5 + - - -
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Residues in contact with MET 449 (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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311A TYR* 3.7 46.0 - - + +
313A LEU* 4.3 11.7 - - + -
443A VAL* 3.6 19.5 - - + +
445A SER 3.1 16.2 + - - +
446A LYS* 3.4 14.8 - - + +
447A HIS 3.2 0.4 - - - -
448A SER* 1.3 77.4 - - - +
450A ASN* 1.3 57.1 + - - +
452A LEU* 3.4 7.5 + - + +
453A ASN* 2.9 67.1 + - - +
456A GLN* 5.1 2.5 - - - +
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Residues in contact with ASN 450 (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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446A LYS* 2.9 21.7 + - - +
447A HIS* 3.0 20.7 + - + +
449A MET* 1.3 74.8 - - - +
451A ILE* 1.3 67.7 + - + +
453A ASN* 3.1 12.1 + - - +
454A ARG* 2.9 48.2 + - + +
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Residues in contact with ILE 451 (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 LEU* 4.3 15.9 - - + -
411A PRO 4.9 1.1 - - - +
412A VAL* 3.6 28.0 - - + -
416A GLY 5.1 1.8 - - - +
418A PRO* 3.7 38.8 - - + +
447A HIS* 3.6 33.4 - - + +
448A SER* 3.1 24.4 + - - +
450A ASN* 1.3 77.5 - - + +
452A LEU* 1.3 63.7 + - - +
454A ARG* 3.2 3.9 + - - +
455A ILE* 3.0 35.2 + - + +
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Residues in contact with LEU 452 (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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311A TYR* 3.6 40.6 - - + -
410A LEU* 4.1 13.9 - - + +
423A TYR* 4.4 8.7 - - + -
441A ASN* 3.7 21.8 - - + +
443A VAL* 3.7 17.0 - - + -
448A SER 3.2 8.0 + - - +
449A MET* 3.6 15.9 - - + +
450A ASN 3.2 0.2 - - - -
451A ILE* 1.3 81.1 - - - +
453A ASN* 1.3 58.5 + - - +
455A ILE* 3.4 12.7 + - + +
456A GLN* 2.9 29.8 + - - +
463A ILE* 3.6 26.6 - - + +
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Residues in contact with ASN 453 (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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449A MET* 2.9 51.9 + - - +
450A ASN* 3.1 13.8 + - - +
452A LEU* 1.3 73.8 - - - +
454A ARG* 1.3 67.2 + - + +
456A GLN* 3.3 21.8 + - - +
457A GLU* 3.2 25.8 + - - +
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Residues in contact with ARG 454 (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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418A PRO* 4.3 18.4 - - + -
420A ASN* 4.5 2.0 + - - +
450A ASN* 2.9 43.1 + - - +
451A ILE* 3.6 7.2 - - - +
453A ASN* 1.3 76.2 - - - +
455A ILE* 1.3 61.2 + - - +
457A GLU* 3.5 3.8 + - - +
458A HIS* 3.0 27.2 + - - +
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Residues in contact with ILE 455 (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 LEU* 5.5 0.9 - - + -
411A PRO* 4.6 11.9 - - + +
418A PRO* 3.9 11.9 - - + -
419A ASP 5.2 0.7 - - - +
420A ASN* 3.5 22.4 - - - +
423A TYR* 3.8 54.7 - - + -
451A ILE* 3.0 29.9 + - + +
452A LEU* 3.5 16.6 - - + +
453A ASN 3.3 0.2 - - - -
454A ARG* 1.3 75.0 - - - +
456A GLN* 1.3 66.5 + - - +
458A HIS* 3.0 11.4 + - - +
459A PHE* 3.1 25.1 + - + -
463A ILE* 5.4 1.6 - - + -
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Residues in contact with GLN 456 (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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311A TYR* 5.8 1.6 - - - -
449A MET* 5.1 3.0 - - - +
452A LEU* 2.9 11.7 + - - +
453A ASN* 3.3 37.8 + - - +
455A ILE* 1.3 79.1 - - - +
457A GLU* 1.3 61.1 + - + +
459A PHE* 3.7 1.3 - - - -
460A ASN* 2.7 25.5 + - - -
461A LYS 2.9 34.5 + - - +
462A LYS* 3.1 21.1 + - - +
463A ILE* 2.7 45.8 + - + +
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Residues in contact with GLU 457 (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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453A ASN 3.2 13.8 + - - +
454A ARG* 3.8 3.1 - - - +
455A ILE 3.2 0.2 - - - -
456A GLN* 1.3 91.1 - - + +
458A HIS* 1.3 65.9 + - - +
460A ASN* 3.3 31.7 + - - +
462A LYS* 5.4 5.0 + - - +
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Residues in contact with HIS 458 (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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299A ARG* 3.1 62.3 + - - +
420A ASN* 3.0 41.4 + - + +
421A GLU* 4.9 1.6 - - - -
454A ARG 3.0 14.9 + - - +
455A ILE 3.0 8.9 + - - +
457A GLU* 1.3 80.5 - - - +
459A PHE* 1.3 73.3 + + - +
460A ASN* 3.6 1.6 + - - +
477A GOL 2.7 42.0 + - - -
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Residues in contact with PHE 459 (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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299A ARG* 4.5 15.2 - - + +
300A GLU* 5.4 3.1 - - - -
302A GLU* 3.7 8.5 - - + -
303A THR* 3.7 30.6 - - + +
309A GLN* 6.2 0.2 - - - +
420A ASN* 3.2 29.4 - - + -
423A TYR* 4.1 12.8 - + - -
424A LEU* 3.6 30.1 - - + -
455A ILE* 3.1 38.8 + - + +
456A GLN* 4.4 1.1 - - - +
458A HIS* 1.3 90.6 - + - +
460A ASN* 1.3 70.6 + - - +
461A LYS* 3.3 11.8 + - + +
477A GOL 3.2 25.6 - - - -
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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