Contacts of the strand formed by residues 69 - 77 (chain D) in PDB entry 1ZXN
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 69 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D VAL 3.3 4.0 - - - +
64D TYR* 3.5 36.7 - - - -
65D ASP 2.9 14.8 + - - -
68D VAL* 1.3 74.7 - - - +
70D ILE* 1.3 57.9 + - - -
71D ASN* 2.5 33.0 + - - -
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Residues in contact with ILE 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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62D TRP* 4.2 15.6 - - + -
63D VAL 3.5 9.2 - - - +
64D TYR* 3.8 9.3 - - + +
68D VAL* 5.4 0.5 - - - +
69D GLY* 1.3 67.8 - - - -
71D ASN* 1.3 60.2 + - - +
241D ARG* 6.1 3.4 - - + -
273D MET* 3.9 42.8 - - + +
274D TYR* 5.0 11.9 - - + -
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Residues in contact with ASN 71 (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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61D MET 4.0 0.3 - - - +
62D TRP* 3.4 11.1 - - - -
63D VAL* 3.1 25.3 + - - +
65D ASP* 3.3 25.4 + - - +
68D VAL* 3.6 19.5 - - + +
69D GLY 2.5 25.7 + - - -
70D ILE* 1.3 74.6 - - - +
72D TYR* 1.3 62.4 + - - +
73D ARG* 3.0 31.4 + - - +
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Residues in contact with TYR 72 (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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60D GLN* 3.3 50.7 + - + +
61D MET* 3.9 16.4 - - - -
62D TRP* 3.2 58.2 - + + -
71D ASN* 1.3 74.8 - - - +
73D ARG* 1.3 68.2 + - - +
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Residues in contact with ARG 73 (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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60D GLN* 2.8 37.1 + - - +
61D MET 3.1 16.1 + - - +
63D VAL* 3.9 10.4 - - + +
65D ASP* 2.7 42.4 + - - -
71D ASN* 3.0 28.7 - - - +
72D TYR* 1.3 78.2 - - - +
74D GLU* 1.3 80.0 + - - +
75D VAL* 4.1 7.5 - - + +
233D LYS* 5.3 1.2 + - - +
234D ASP* 2.5 37.0 + - - -
237D ALA* 4.5 3.6 - - - +
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Residues in contact with GLU 74 (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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58D THR* 3.5 31.4 - - + +
59D GLN 3.2 9.9 - - - +
60D GLN* 3.9 15.6 + - + +
73D ARG* 1.3 92.3 + - - +
75D VAL* 1.3 68.1 + - - +
234D ASP* 4.4 0.5 - - - +
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Residues in contact with VAL 75 (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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57D VAL 3.1 1.8 - - - +
58D THR* 2.9 7.8 - - - -
59D GLN 2.6 36.6 + - - +
61D MET* 4.0 27.4 - - + +
63D VAL* 4.1 17.5 - - + -
73D ARG* 4.1 13.9 - - - +
74D GLU* 1.3 84.1 - - - +
76D THR* 1.3 66.6 + - - +
77D PHE* 3.7 23.5 - - + -
234D ASP* 3.4 32.5 - - + +
238D LEU* 5.3 2.2 - - + -
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Residues in contact with THR 76 (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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56D LEU* 3.4 36.9 - - + +
57D VAL 3.1 7.2 - - - +
58D THR* 2.5 24.3 + - - +
75D VAL* 1.3 73.4 - - - +
77D PHE* 1.3 64.3 + - - +
232D ASP* 4.4 7.6 - - - +
234D ASP* 3.3 24.8 + - - +
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Residues in contact with PHE 77 (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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56D LEU* 3.3 13.4 - - - -
57D VAL* 3.0 48.6 + - + +
59D GLN* 4.2 6.7 - - - -
61D MET* 3.5 40.4 - - + -
75D VAL* 3.7 23.1 - - + -
76D THR* 1.3 77.0 - - - +
78D VAL* 1.3 77.8 + - - +
79D PRO* 3.9 21.8 - - + -
82D TYR* 4.1 22.9 - + + -
228D MET* 4.5 4.7 - - - -
235D ILE* 4.5 26.0 - - + -
238D LEU* 5.1 8.5 - - + -
379D GLU* 6.1 0.4 - - - -
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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