Contacts of the helix formed by residues 418 - 422 (chain B) in PDB entry 3N9Z
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 TRP 418 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B PHE* 3.3 76.5 - + + -
73B LYS* 5.2 7.4 - - + -
75B GLU* 3.4 19.5 - - + +
355B LEU* 4.8 0.2 - - - +
357B ARG* 3.2 21.3 + - - +
411B PHE* 3.6 15.6 - + - -
414B LEU* 4.9 3.8 - - + -
417B GLY* 1.3 76.1 - - - +
419B GLY* 1.3 86.6 + - - +
420B VAL 4.0 0.2 + - - -
421B ARG 4.2 0.2 + - - -
422B GLN* 3.5 10.9 + - - +
426B ARG* 5.6 0.4 - - - +
601B HEM 3.4 5.9 + - - -
53D SER* 3.9 18.9 + - - -
54D THR* 6.1 5.2 - - + -
77D MET* 6.0 0.9 - - + -
80D LEU* 3.1 58.4 - - + +
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Residues in contact with GLY 419 (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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75B GLU* 4.4 1.1 - - - -
418B TRP* 1.3 100.3 - - - +
420B VAL* 1.3 63.3 + - - -
422B GLN* 2.9 21.1 + - - +
51D ALA 2.9 17.6 - - - +
52D CYS* 4.3 11.9 - - - +
53D SER* 5.5 1.3 - - - -
77D MET* 5.5 2.4 - - - +
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLU* 4.5 5.6 + - - +
76B GLY 5.1 2.2 - - - +
77B PRO* 4.1 9.2 - - + +
79B PRO* 3.8 30.5 - - + -
108B TRP* 3.7 17.2 - - + -
109B LYS* 5.0 4.0 - - - +
112B ARG* 3.5 23.5 + - + +
116B ASN* 4.9 2.8 + - - -
419B GLY* 1.3 71.8 - - - -
421B ARG* 1.3 60.9 + - - +
422B GLN 3.5 0.7 - - - -
45D ALA* 3.5 36.1 - - + +
46D CYS* 4.0 11.0 - - + +
51D ALA 3.8 6.3 - - - +
52D CYS* 3.6 15.3 - - + -
54D THR* 5.4 1.8 - - + -
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Residues in contact with ARG 421 (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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75B GLU* 5.3 0.2 + - - -
79B PRO* 3.0 44.1 + - + +
80B GLU* 4.1 9.6 - - - +
81B ARG* 2.9 33.7 + - - +
83B LEU* 5.3 3.0 - - - +
100B VAL 3.0 20.4 + - - -
101B LEU 3.2 15.4 + - - -
103B LYS 2.8 30.4 + - - -
104B LYS* 4.4 5.7 - - - +
108B TRP* 3.2 34.5 - - + +
112B ARG* 3.8 2.9 + - - +
357B ARG* 4.1 14.8 - - - +
418B TRP 4.2 1.4 + - - -
419B GLY 3.2 0.6 - - - -
420B VAL* 1.3 78.9 - - - +
422B GLN* 1.3 62.9 + - - +
601B HEM 2.7 26.3 + - - +
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Residues in contact with GLN 422 (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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112B ARG* 2.9 28.1 + - - +
120B MET* 4.1 12.1 - - + +
416B PHE 3.4 11.0 - - - +
418B TRP 3.5 15.0 + - - +
419B GLY 2.9 17.0 + - - +
420B VAL 3.5 0.4 - - - -
421B ARG* 1.3 78.9 - - - +
423B CYS* 1.3 72.4 + - - +
424B LEU 3.2 0.3 + - - -
426B ARG* 2.9 49.5 - - - +
427B ARG* 5.1 0.6 - - - +
601B HEM 3.7 11.3 - - - +
51D ALA 2.9 27.5 - - - +
77D MET* 3.7 16.5 - - - +
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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