Contacts of the helix formed by residues 58 - 71 (chain N) in PDB entry 6PSU
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 CYS 58 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268I ARG* 5.8 0.2 - - - -
270I THR* 5.9 4.0 - - - -
37N CYS* 2.9 18.7 - - + +
40N CYS* 4.1 3.1 - - - -
42N ASN 5.0 0.2 - - - +
43N PRO 4.5 9.2 - - - +
44N ILE* 3.2 15.4 - - + +
45N PRO* 5.4 4.0 - - + -
48N ARG* 4.0 3.8 - - - +
57N LEU* 1.3 77.4 - - - +
59N VAL* 1.3 69.4 + - + +
60N GLU* 3.1 20.4 + - - -
61N CYS 3.5 4.1 + - - -
62N GLN* 3.1 19.6 + - - +
101N ZN 2.4 34.8 - - - -
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Residues in contact with VAL 59 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272I ARG* 6.2 2.9 - - - +
671J GLY* 4.4 17.7 - - - +
672J LEU 4.2 3.4 - - - +
673J VAL 4.0 25.1 - - - +
674J THR* 4.1 4.8 - - + +
48N ARG* 3.1 28.9 - - - +
58N CYS* 1.3 74.8 - - + +
60N GLU* 1.3 75.0 + - + +
62N GLN* 3.9 1.0 - - - +
63N ALA* 2.9 31.7 + - + +
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Residues in contact with GLU 60 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247I ARG* 4.8 6.9 + - - -
248I GLY* 4.3 10.2 + - - -
268I ARG* 4.2 12.2 + - + +
269I ILE 2.7 24.9 - - - +
270I THR* 3.0 38.9 - - + +
271I ALA* 3.2 10.4 + - - +
272I ARG* 5.6 1.4 + - - -
58N CYS* 3.1 11.0 + - - -
59N VAL* 1.3 89.1 - - + +
61N CYS* 1.3 65.7 + - - +
63N ALA* 3.1 7.6 + - - +
64N TYR* 2.9 26.7 + - - +
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Residues in contact with CYS 61 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268I ARG* 3.7 35.4 - - - +
37N CYS* 3.3 15.7 - - - -
39N ALA* 3.3 30.3 - - + -
40N CYS 4.2 1.8 - - - -
57N LEU* 3.8 7.8 - - + +
58N CYS* 3.5 2.2 + - - -
60N GLU* 1.3 75.9 - - - +
62N GLN* 1.3 57.2 + - - +
64N TYR* 3.3 5.0 + - - +
65N GLN* 2.9 28.1 + - - +
101N ZN 2.6 30.5 - - - -
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Residues in contact with GLN 62 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674J THR* 3.8 15.3 - - + +
677J GLU* 3.5 25.8 + - - +
48N ARG* 2.2 36.9 + - - +
55N VAL* 4.2 10.9 - - - +
57N LEU* 3.5 23.1 - - + +
58N CYS 3.1 17.5 + - - +
59N VAL 4.0 2.0 - - - +
61N CYS* 1.3 78.4 - - - +
63N ALA* 1.3 55.9 + - - +
65N GLN* 3.2 3.1 + - + +
66N GLU* 2.8 38.6 + - + +
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Residues in contact with ALA 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674J THR* 3.7 15.2 - - + +
59N VAL* 2.9 22.7 + - + +
60N GLU* 3.1 7.4 + - - +
62N GLN* 1.3 75.8 - - - +
64N TYR* 1.3 63.4 + - - +
66N GLU* 3.3 4.8 + - - +
67N ARG* 2.9 32.3 + - - +
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Residues in contact with TYR 64 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248I GLY 5.3 2.9 - - - -
268I ARG* 3.8 34.1 - - - +
340I ASP* 3.2 27.1 + - - -
341I LEU* 3.3 48.5 - - + -
60N GLU 2.9 14.0 + - - +
61N CYS 3.4 9.0 - - - +
62N GLN 3.2 0.2 - - - -
63N ALA* 1.3 75.9 - - - +
65N GLN* 1.3 60.4 + - + +
67N ARG* 3.3 6.1 + - - +
68N GLN* 2.9 54.6 + - + +
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Residues in contact with GLN 65 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57N LEU* 3.5 21.1 - - - +
61N CYS 2.9 16.2 + - - +
62N GLN* 3.2 6.5 + - + +
64N TYR* 1.3 77.8 - - + +
66N GLU* 1.3 63.0 + - - +
68N GLN* 3.7 7.0 - - + +
69N ARG* 2.9 47.7 + - + +
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Residues in contact with GLU 66 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674J THR* 4.3 20.9 - - + +
676J GLY* 4.1 25.1 - - - +
677J GLU* 4.2 9.2 - - - +
26N LYS* 4.2 20.2 + - - -
62N GLN* 2.8 29.8 + - + +
63N ALA* 3.5 7.2 - - - +
65N GLN* 1.3 79.9 - - - +
67N ARG* 1.3 58.0 + - - +
69N ARG* 3.7 7.2 - - - +
70N LYS* 2.9 29.3 + - - +
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Residues in contact with ARG 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341I LEU* 3.6 38.5 - - + +
342I ASP* 5.6 4.9 - - - -
437I ASN 5.7 0.9 - - - -
438I GLY* 4.6 17.5 + - - -
63N ALA* 2.9 25.5 + - - +
64N TYR 3.7 4.0 - - - +
66N GLU* 1.3 76.5 - - - +
68N GLN* 1.3 62.9 + - - +
70N LYS* 3.4 18.0 - - + +
71N HIS* 3.3 28.7 + - + -
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Residues in contact with GLN 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340I ASP* 3.5 25.5 + - - +
341I LEU* 3.9 13.1 + - - +
64N TYR* 2.9 53.6 + - + +
65N GLN* 3.7 7.2 - - + +
66N GLU 3.2 0.2 - - - -
67N ARG* 1.3 76.0 - - + +
69N ARG* 1.3 70.0 + - + +
70N LYS 3.3 0.5 + - - -
71N HIS* 3.4 16.9 + - - +
72N TYR 3.9 3.3 + - - -
73N ALA 4.3 14.4 + - - +
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Residues in contact with ARG 69 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161I LYS* 5.2 0.5 + - - -
65N GLN* 2.9 39.8 + - + +
66N GLU* 4.0 9.6 - - - +
68N GLN* 1.3 75.7 + - - +
70N LYS* 1.3 56.5 + - - +
72N TYR* 2.6 58.5 + - - +
73N ALA* 4.2 21.2 - - - +
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Residues in contact with LYS 70 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161I LYS* 3.7 18.8 + - - +
170I VAL* 4.8 1.4 - - - +
172I TYR* 4.1 9.1 + - - +
435I ILE 4.4 3.2 + - - -
438I GLY* 3.2 38.7 - - - +
440I GLY 5.0 3.4 + - - -
441I GLU* 4.8 11.9 - - - -
66N GLU 2.9 14.5 + - - +
67N ARG* 3.4 20.4 - - + +
68N GLN 3.1 0.6 - - - -
69N ARG* 1.3 76.0 - - - +
71N HIS* 1.3 78.3 + - + +
72N TYR 3.3 1.0 + - - -
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Residues in contact with HIS 71 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169I LYS* 4.6 14.7 - - - +
170I VAL* 3.2 27.0 + - + +
172I TYR* 3.0 32.9 + + + +
341I LEU 5.9 2.2 - - - -
435I ILE 4.0 0.2 + - - -
436I ARG* 3.0 36.6 + - - +
437I ASN 4.5 0.2 - - - -
438I GLY* 3.1 33.5 + - - -
67N ARG* 3.3 20.9 + - + -
68N GLN* 3.4 8.7 + - - +
69N ARG 3.1 0.8 - - - -
70N LYS* 1.3 84.7 + - + +
72N TYR* 1.3 63.3 + - - +
73N ALA* 3.0 12.8 + - - +
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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