Contacts of the strand formed by residues 68 - 76 (chain A) in PDB entry 3ZLY
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 PHE 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.7 22.7 - - + -
64A LYS 3.3 27.8 - - - -
65A ASP 3.3 9.8 + - - +
66A ASP* 3.3 2.2 - - - +
67A ASP* 1.3 78.3 - - - +
69A GLU* 1.3 60.1 + - - +
70A LYS 4.2 0.8 + - - -
85A VAL* 3.6 30.7 - - + -
86A SER 3.3 8.5 - - - -
87A HIS* 3.8 16.2 - + + -
88A LYS* 3.9 10.6 + - - -
94A MET* 3.7 23.8 - - - -
96A ARG* 3.7 23.0 + - - +
133A PHE* 3.6 26.2 - + - -
142A CYS* 3.6 20.6 - - - -
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A PHE* 1.3 73.4 - - - +
70A LYS* 1.3 74.1 + - - +
71A ILE* 3.4 3.2 + - + +
85A VAL* 3.3 3.6 - - - -
86A SER* 2.8 52.2 + - - +
88A LYS* 3.9 29.3 + - + +
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Residues in contact with LYS 70 (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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68A PHE 4.2 1.8 + - - -
69A GLU* 1.3 81.8 + - - +
71A ILE* 1.4 62.8 + - - +
72A SER* 4.2 15.7 - - - +
73A GLU* 4.7 2.3 - - - +
83A PHE* 3.5 49.6 - - + -
84A LYS 3.9 3.6 - - - -
85A VAL* 4.1 9.3 - - + +
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Residues in contact with ILE 71 (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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69A GLU* 4.0 10.3 - - + +
70A LYS* 1.4 78.6 - - - +
72A SER* 1.3 69.4 + - - +
84A LYS* 2.8 44.2 + - + +
85A VAL 3.7 22.4 - - - +
86A SER* 3.9 12.8 - - - +
93A VAL* 4.4 11.0 - - + -
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Residues in contact with SER 72 (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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70A LYS* 3.9 8.0 - - - +
71A ILE* 1.3 82.3 - - - +
73A GLU* 1.3 64.0 + - - +
74A LEU* 4.9 2.3 - - - +
83A PHE* 3.3 11.7 - - - +
84A LYS* 2.7 51.2 + - - +
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Residues in contact with GLU 73 (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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70A LYS* 4.7 3.0 - - - +
72A SER* 1.3 80.7 + - - +
74A LEU* 1.3 64.9 + - - +
75A GLY* 3.9 17.4 - - - +
76A ALA* 4.2 7.0 + - - +
81A VAL* 3.6 25.5 - - + +
82A VAL 3.6 12.3 - - - +
83A PHE* 3.9 17.9 - - + -
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Residues in contact with LEU 74 (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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72A SER* 4.9 2.0 - - - +
73A GLU* 1.3 75.8 - - - +
75A GLY* 1.3 51.9 + - - +
82A VAL* 2.8 15.8 + - + +
83A PHE 3.8 6.3 - - - +
84A LYS* 3.6 44.0 - - + +
95A ALA* 3.9 13.7 - - + -
145A HIS* 3.8 26.2 - - + +
146A MET 5.7 0.2 - - - +
153A GLN* 2.8 31.0 + - - +
1383A YSO 3.4 37.3 + - + +
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Residues in contact with GLY 75 (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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73A GLU* 3.7 11.4 - - - +
74A LEU* 1.3 79.6 - - - +
76A ALA* 1.4 55.9 + - - -
81A VAL* 3.6 5.5 - - - +
82A VAL* 2.8 35.6 + - - +
153A GLN* 4.4 6.7 - - - -
1383A YSO 4.7 4.9 - - - -
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Residues in contact with ALA 76 (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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73A GLU* 4.2 10.7 + - - +
75A GLY* 1.4 73.8 - - - +
77A GLY* 1.3 61.6 + - - +
80A GLY 3.7 7.0 - - - +
81A VAL* 4.5 14.1 - - + -
82A VAL* 5.9 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