Contacts of the helix formed by residues 403 - 412 (chain A) in PDB entry 1H7B
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 GLY 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A LEU* 5.0 0.2 - - - -
320A PRO* 3.5 15.3 - - - +
402A ILE* 1.3 74.6 - - - +
404A ILE* 1.3 66.4 + - - +
405A HIS 3.1 2.7 - - - -
406A GLU* 3.2 14.2 + - - -
407A LEU* 3.0 19.0 + - - +
472A TYR* 4.4 2.0 - - - -
473A THR 2.8 28.9 + - - -
475A SER 3.5 3.0 + - - -
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Residues in contact with ILE 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 4.1 18.8 - - + -
401A TYR* 3.9 10.5 - - + -
402A ILE 3.7 0.2 - - - -
403A GLY* 1.3 72.2 - - - +
405A HIS* 1.3 64.8 + - - +
407A LEU* 3.0 9.8 + - + +
408A ASN* 2.9 41.0 + - - +
416A GLY* 3.9 19.3 - - - -
419A ILE* 4.8 2.9 - - + -
420A LEU* 3.5 40.2 - - + -
475A SER 2.9 17.8 + - - +
476A PHE* 3.9 19.5 - - + +
496A TYR* 4.0 10.8 - - + +
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Residues in contact with HIS 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A GLY* 3.1 0.4 - - - -
404A ILE* 1.3 83.2 - - - +
406A GLU* 1.3 84.3 + - + +
408A ASN* 3.4 9.9 + - - +
409A ILE* 3.3 48.2 + - + +
465A ASP* 4.7 3.0 + - - +
469A LYS* 4.9 4.6 - - - -
473A THR* 3.8 17.0 - - + -
475A SER 4.5 1.0 + - - -
477A HIS 4.3 8.8 + - - +
478A VAL* 5.6 0.6 - - - -
479A SER* 3.4 36.4 + - - -
481A GLU* 5.5 2.4 + - - -
482A GLU* 4.9 12.6 + - + -
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Residues in contact with GLU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PRO* 3.8 17.0 - - + -
403A GLY* 3.2 14.1 + - - -
405A HIS* 1.3 76.1 - - - +
407A LEU* 1.3 61.9 + - - +
408A ASN 3.4 0.2 - - - -
409A ILE* 3.8 7.4 - - - +
410A LEU* 3.1 32.0 + - - +
465A ASP 3.9 4.7 - - - +
466A VAL* 3.9 21.6 - - + +
469A LYS* 2.5 35.6 + - - +
472A TYR* 3.8 14.8 - - + -
473A THR* 2.9 43.5 + - - -
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Residues in contact with LEU 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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319A LEU* 3.5 43.1 - - + +
320A PRO* 4.3 3.3 - - - +
323A ALA* 3.8 16.8 - - + -
337A PHE* 3.8 19.7 - - + -
403A GLY 3.0 12.1 + - - +
404A ILE* 3.0 12.4 + - + +
406A GLU* 1.3 74.5 - - - +
408A ASN* 1.3 63.6 + - - +
410A LEU* 3.2 7.3 + - - +
411A VAL* 2.9 31.4 + - + +
415A ILE* 3.7 27.1 - - + -
419A ILE* 4.2 22.9 - - + -
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Residues in contact with ASN 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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404A ILE* 2.9 32.0 + - - +
405A HIS* 3.6 11.8 + - - +
407A LEU* 1.3 75.2 - - - +
409A ILE* 1.3 65.7 + - + +
411A VAL* 3.3 1.5 + - - -
412A GLY 3.0 20.6 + - - -
413A ARG 3.2 20.4 + - - +
414A ASP* 3.4 27.5 + - - +
415A ILE* 2.9 26.0 + - - +
416A GLY 3.5 6.2 + - - -
496A TYR* 5.4 0.2 + - - -
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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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327A TYR* 4.7 1.6 + - - -
405A HIS* 3.3 41.3 + - + +
406A GLU* 3.8 8.1 - - - +
407A LEU 3.2 0.2 - - - -
408A ASN* 1.3 80.3 - - + +
410A LEU* 1.3 61.3 + - + +
411A VAL 3.5 0.2 + - - -
412A GLY* 3.6 8.4 + - - -
464A LYS 4.5 3.1 - - - +
465A ASP* 3.6 40.6 - - + +
466A VAL* 4.2 12.8 - - + -
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Residues in contact with LEU 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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320A PRO* 3.4 36.6 - - + +
323A ALA* 3.7 16.4 - - + -
324A LEU* 3.8 28.3 - - + -
327A TYR* 2.8 42.2 + - + +
332A PHE* 3.9 6.6 - - - +
406A GLU 3.1 21.7 + - - +
407A LEU* 3.2 6.0 + - - +
409A ILE* 1.3 79.3 - - + +
411A VAL* 1.3 59.3 + - - +
412A GLY 3.4 0.2 - - - -
463A VAL* 4.3 8.3 - - + -
466A VAL* 3.2 27.1 - - + -
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Residues in contact with VAL 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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323A ALA* 4.1 2.7 - - + -
332A PHE* 3.5 49.3 - - + -
337A PHE* 4.5 1.8 - - + -
407A LEU* 2.9 32.6 + - + +
408A ASN 3.6 0.4 - - - +
410A LEU* 1.3 79.5 - - - +
412A GLY* 1.3 58.9 + - - +
413A ARG* 3.4 36.0 + - - +
415A ILE* 3.4 35.9 - - + -
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Residues in contact with GLY 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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408A ASN 3.0 8.2 + - - -
409A ILE 3.6 6.3 + - - -
410A LEU 3.4 3.2 - - - -
411A VAL* 1.3 77.9 - - - +
413A ARG* 1.3 62.8 + - - +
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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