Contacts of the helix formed by residues 57 - 71 (chain D) in PDB entry 1ZWS
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 57 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220C ASP* 4.8 1.6 - - - -
221C THR* 4.8 3.1 - - - +
47D ARG* 3.0 31.6 - - - +
56D VAL* 1.3 76.5 - - - +
58D ARG* 1.3 63.9 + - - +
59D GLU* 2.9 19.8 + - - +
60D GLU* 2.9 33.6 + - - +
61D ILE* 2.8 27.5 + - - +
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Residues in contact with ARG 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D PRO* 6.3 0.2 - - - +
4D PHE* 3.4 25.4 - - - -
46D LYS* 6.0 5.2 - - - +
56D VAL 3.7 1.0 + - - -
57D SER* 1.3 69.9 + - - +
59D GLU* 1.3 70.0 + - - +
61D ILE* 3.1 12.6 - - - +
62D GLU* 2.9 77.2 + - - +
84D GLU* 3.4 25.6 + - - -
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C THR* 5.4 7.5 - - + +
223C GLN* 5.1 1.4 + - - -
57D SER* 2.9 9.6 + - - +
58D ARG* 1.3 78.0 - - - +
60D GLU* 1.3 54.0 + - + +
61D ILE 2.6 6.9 + - - -
62D GLU* 2.7 10.5 + - - -
63D ARG* 2.6 73.5 + - + +
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Residues in contact with GLU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C ASP 4.1 3.1 - - - +
221C THR* 3.3 24.0 - - + +
47D ARG* 4.1 1.9 + - - -
56D VAL* 3.2 22.2 - - + +
57D SER* 2.9 36.5 + - - +
59D GLU* 1.3 78.7 - - - +
61D ILE* 1.3 62.7 + - - +
63D ARG* 3.0 35.6 + - - +
64D GLU* 3.2 21.0 + - - +
163D GLY 5.4 4.0 - - - +
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Residues in contact with ILE 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D PHE* 4.5 14.4 - - + -
44D ILE* 3.2 42.6 - - + +
46D LYS* 5.3 3.1 - - + -
56D VAL* 3.8 15.7 - - + +
57D SER 2.8 26.6 + - - +
58D ARG* 3.1 16.6 - - - +
59D GLU 2.6 3.8 + - - -
60D GLU* 1.3 69.8 - - - +
62D GLU* 1.3 63.8 + - + +
64D GLU* 2.7 28.3 + - - +
65D VAL* 3.0 26.0 + - + +
89D VAL* 4.2 26.5 - - + -
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Residues in contact with GLU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D PHE* 4.6 6.7 - - + -
58D ARG* 3.0 58.8 + - - +
59D GLU* 2.7 9.8 + - - +
61D ILE* 1.3 77.6 - - - +
63D ARG* 1.3 56.9 + - - +
65D VAL* 3.0 7.9 + - - -
66D SER* 2.6 39.2 + - - -
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Residues in contact with ARG 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C THR* 5.0 4.6 - - - +
223C GLN* 3.6 18.6 - - - +
59D GLU* 2.6 50.6 + - + +
60D GLU* 3.0 39.9 + - - +
62D GLU* 1.3 73.7 - - - +
64D GLU* 1.3 51.9 + - - +
66D SER* 4.2 4.6 - - - -
67D ILE* 2.6 44.3 + - + +
163D GLY 5.8 2.0 + - - -
165D ALA 4.7 12.2 + - - +
166D HIS* 3.4 44.2 + - - -
167D GLU* 5.4 2.9 - - + +
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Residues in contact with GLU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LYS* 2.9 31.3 + - - +
44D ILE* 4.1 14.7 - - + +
60D GLU 3.2 13.3 + - - +
61D ILE* 2.7 17.7 + - - +
63D ARG* 1.3 70.3 - - - +
65D VAL* 1.3 60.5 + - + +
67D ILE* 3.2 6.5 - - - +
68D LEU* 2.9 44.2 + - + +
91D LEU* 4.1 11.0 - - - +
93D LEU* 5.8 0.3 - - - +
162D PHE* 3.2 37.7 + - + +
163D GLY* 3.7 12.4 - - - +
165D ALA 6.0 1.1 - - - -
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Residues in contact with VAL 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D PHE* 3.9 24.7 - - + -
44D ILE* 6.1 1.3 - - + -
61D ILE* 3.0 23.7 + - + +
62D GLU* 3.6 6.1 - - - +
64D GLU* 1.3 74.1 - - + +
66D SER* 1.3 68.3 + - - +
67D ILE 3.1 0.2 + - - -
68D LEU* 3.2 8.6 + - - +
69D ARG* 2.9 55.9 + - + +
79D LEU* 4.5 2.5 - - + -
82D VAL* 4.2 11.0 - - + -
89D VAL* 5.5 0.7 - - + -
91D LEU* 4.0 26.5 - - + -
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Residues in contact with SER 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D GLU* 2.6 24.4 + - - -
63D ARG* 4.2 4.9 - - - -
65D VAL* 1.3 75.7 - - - +
67D ILE* 1.3 68.2 + - - +
69D ARG* 3.2 11.2 + - - +
70D GLN* 3.1 34.2 + - - +
167D GLU* 5.5 0.7 + - - -
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Residues in contact with ILE 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ARG* 2.6 29.8 - - + +
64D GLU* 3.2 9.0 - - - +
65D VAL 3.1 0.2 - - - -
66D SER* 1.3 74.9 - - - +
68D LEU* 1.3 61.1 + - - +
70D GLN* 2.5 38.7 + - - +
71D VAL* 3.3 12.5 + - + +
135D ILE* 4.1 37.0 - - + -
162D PHE* 4.4 22.4 - - + -
165D ALA* 4.8 8.3 - - + +
166D HIS* 4.7 3.8 - - - +
167D GLU* 4.2 34.3 - - + +
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Residues in contact with LEU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D GLU* 2.9 38.0 + - + +
65D VAL* 3.7 4.5 - - - +
67D ILE* 1.3 76.2 - - - +
69D ARG* 1.3 58.2 + - - +
71D VAL* 2.8 36.3 - - + +
77D ILE* 4.4 16.1 - - + +
78D THR 6.2 0.2 - - - -
79D LEU* 4.1 27.1 + - + +
91D LEU* 4.5 10.1 - - + -
93D LEU* 4.0 28.9 - - + -
162D PHE* 3.8 38.8 - - + -
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Residues in contact with ARG 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D GLU* 3.2 43.5 + - - +
3D PRO 3.8 9.1 + - - -
4D PHE* 4.0 15.0 - - - -
65D VAL* 2.9 31.3 + - - +
66D SER* 3.3 12.4 - - - +
67D ILE 2.7 4.6 + - - -
68D LEU* 1.3 75.8 - - - +
70D GLN* 1.3 60.1 + - + +
71D VAL 3.3 5.9 + - - +
72D LEU* 5.3 1.9 - - - +
79D LEU* 3.8 18.5 - - + +
82D VAL* 4.2 13.3 + - - +
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Residues in contact with GLN 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D SER* 3.1 28.2 + - - +
67D ILE* 2.5 22.0 + - - +
69D ARG* 1.3 73.0 - - + +
71D VAL* 1.3 60.6 + - + +
72D LEU* 3.8 1.7 + - - +
129D TYR* 3.6 3.8 + - - -
133D LYS* 3.3 48.5 + - + +
135D ILE* 5.0 10.0 - - + +
167D GLU* 3.8 21.2 + - - +
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Residues in contact with VAL 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ILE* 4.2 7.6 - - + +
68D LEU* 2.8 55.3 - - + +
69D ARG 3.8 3.5 - - - +
70D GLN* 1.3 77.3 - - - +
72D LEU* 1.3 66.0 + - - +
73D HIS 4.0 0.7 - - - -
76D VAL* 4.3 19.3 - - + -
77D ILE 4.7 4.2 - - - +
78D THR* 4.9 6.4 - - - +
79D LEU 5.8 0.2 + - - -
129D TYR* 3.7 16.8 - - + -
130D LEU* 3.9 27.8 - - + -
133D LYS* 5.4 2.0 - - + -
135D ILE* 4.5 15.3 - - + -
162D PHE* 5.3 1.8 - - + -
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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