Contacts of the helix formed by residues 449 - 456 (chain A) in PDB entry 3N1Z
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 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A ILE* 5.6 0.4 - - - -
396A ILE* 3.2 40.5 + - + +
397A CYS 4.1 1.3 + - - +
398A ASN* 3.1 25.6 + - - +
401A ASN* 3.4 24.7 - - - +
447A HIS* 3.9 2.7 + - + -
448A THR* 1.3 78.9 - - - +
450A LEU* 1.3 63.3 + - - +
451A VAL* 2.7 22.2 + - - +
452A ASP* 2.7 26.4 + - - +
453A ARG* 3.1 21.7 + - - +
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Residues in contact with LEU 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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165A ASN 3.9 8.3 - - - +
167A TRP* 4.0 19.1 - - + -
170A ILE* 4.3 16.4 - - + +
393A LEU* 4.8 5.2 - - + -
396A ILE* 4.6 11.7 - - + +
401A ASN* 4.8 1.0 + - - -
449A ASN* 1.3 74.7 + - - +
451A VAL* 1.3 65.1 + - - +
453A ARG* 3.2 9.3 + - - +
454A PHE* 2.9 22.3 + - - +
459A ILE* 4.2 8.9 - - + +
467A ALA* 6.3 1.3 - - + -
470A TYR* 3.6 34.1 - - + -
471A MET* 3.6 32.8 - - + -
502A P6G 4.3 14.4 - - - -
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Residues in contact with VAL 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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393A LEU* 4.2 18.4 - - + -
394A PRO 3.2 26.7 - - - +
395A THR* 4.5 2.0 - - - -
396A ILE* 3.9 17.4 - - + +
449A ASN* 2.7 16.3 + - - +
450A LEU* 1.3 74.7 - - - +
452A ASP* 1.3 57.1 + - - +
454A PHE* 3.0 8.2 + - - +
455A LEU* 2.7 56.4 + - + +
7C MET* 3.9 18.6 - - + -
18C LEU* 4.7 9.0 - - + -
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Residues in contact with ASP 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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398A ASN* 3.1 14.6 + - - +
424A ARG* 2.9 28.2 + - - +
425A LEU 5.5 2.6 - - - +
448A THR* 3.7 12.1 - - + -
449A ASN* 2.7 41.6 + - - +
451A VAL* 1.3 81.4 - - - +
453A ARG* 1.3 58.3 + - - +
455A LEU* 3.4 6.4 + - - +
456A LYS* 3.0 38.6 + - + +
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Residues in contact with ARG 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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165A ASN* 3.8 21.4 + - - +
170A ILE* 4.1 20.4 - - - +
447A HIS* 4.1 2.8 + - - -
448A THR* 3.0 42.3 + - - +
449A ASN* 3.1 9.1 + - - +
450A LEU* 3.2 10.9 + - + +
452A ASP* 1.3 73.2 - - - +
454A PHE* 1.3 66.6 + - - +
456A LYS* 3.2 6.8 + - - -
458A GLU* 3.1 53.4 + - + +
459A ILE* 3.8 11.8 + - + -
470A TYR* 3.2 28.7 + - - +
44B ARG* 6.2 1.4 - - - +
47B GLU* 3.1 26.1 + - - -
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Residues in contact with PHE 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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393A LEU* 4.0 31.9 - - + -
450A LEU 2.9 13.7 + - - +
451A VAL* 3.4 7.4 - - - +
453A ARG* 1.3 75.2 - - - +
455A LEU* 1.3 69.7 + - + +
456A LYS 3.0 1.4 + - - -
457A GLY* 3.1 14.0 + - - -
459A ILE* 3.8 31.1 + - + +
462A ALA* 3.3 47.1 - - + +
463A ASP* 3.8 19.1 - - - -
464A LEU* 5.8 1.3 - - + -
467A ALA* 4.6 4.9 - - + -
18C LEU* 4.2 22.0 - - + -
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Residues in contact with LEU 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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451A VAL* 2.7 39.3 + - + +
452A ASP* 3.6 7.4 - - - +
454A PHE* 1.3 79.2 - - + +
456A LYS* 1.3 59.5 + - + +
457A GLY 3.4 0.4 - - - -
5C PRO* 4.0 23.1 - - + -
7C MET* 4.6 0.2 - - + -
18C LEU* 3.9 33.4 - - + -
76C THR* 3.4 24.7 - - - +
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Residues in contact with LYS 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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448A THR* 4.9 18.9 - - + +
452A ASP* 3.0 28.7 + - + +
453A ARG* 3.8 5.4 - - - +
454A PHE 3.0 1.2 + - - -
455A LEU* 1.3 78.9 - - + +
457A GLY* 1.3 60.1 + - - +
458A GLU* 3.1 32.9 + - - +
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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