Contacts of the strand formed by residues 72 - 77 (chain A) in PDB entry 1ZIA
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 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PRO* 3.8 7.2 - - - -
70A ALA 3.8 0.2 + - - -
71A PRO* 1.3 75.4 - - - +
73A VAL* 1.3 64.8 + - - -
74A TYR* 3.7 2.8 - - - -
92A VAL* 2.8 38.2 + - - +
96A PRO* 3.8 18.4 - - - +
97A ALA 4.8 1.8 - - - -
98A ASN* 3.5 11.2 - - - -
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A MET 3.4 6.8 - - - +
50A PRO* 3.4 5.5 - - - +
72A GLY* 1.3 72.1 - - - -
74A TYR* 1.3 67.9 + - - +
89A VAL* 3.4 30.5 - - + -
90A VAL 3.6 3.4 - - - +
91A GLN* 4.1 15.5 - - + +
96A PRO* 3.6 28.7 - - + -
98A ASN* 2.8 31.7 + - - +
99A LEU* 3.9 17.5 - - + -
102A VAL* 3.9 26.8 - - + +
119A LEU* 4.2 2.9 - - + -
122A LEU* 5.6 1.1 - - + -
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Residues in contact with TYR 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 4.7 7.0 - - + -
48A MET 3.2 5.8 - - - -
49A ILE* 4.1 14.1 - - + -
50A PRO* 3.6 24.2 - - + -
53A ALA* 3.4 25.5 - - + +
54A GLU 5.4 2.7 - - - -
56A PHE* 4.9 4.9 - + - -
68A PHE* 3.8 29.8 - + + -
69A THR* 4.2 4.7 + - - -
70A ALA 2.6 37.7 + - - -
72A GLY 3.7 5.8 - - - -
73A VAL* 1.3 78.3 - - - +
75A GLY* 1.3 59.9 + - - +
76A VAL* 3.9 8.6 + - + +
89A VAL* 3.4 3.5 - - - +
90A VAL* 2.8 37.6 + - + +
92A VAL* 3.5 28.5 - - + -
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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
----------------------------------------------------------
44A THR* 3.5 7.6 - - - +
45A ILE* 2.9 33.8 + - - +
48A MET* 2.9 31.7 + - - +
73A VAL* 4.2 1.2 - - - +
74A TYR* 1.3 72.6 - - - +
76A VAL* 1.3 61.4 + - - +
88A GLY 3.6 8.3 - - - -
89A VAL* 4.5 7.2 - - - -
115A LEU* 5.0 0.2 - - - -
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 4.6 7.4 - - + -
33A PHE* 4.4 18.6 - - + -
42A VAL* 3.7 26.7 - - + -
43A GLU 3.3 6.5 - - - +
44A THR* 4.7 3.8 - - + -
45A ILE* 3.5 4.6 - - - +
56A PHE* 4.2 20.0 - - + -
68A PHE* 5.4 1.1 - - + -
74A TYR* 4.5 12.1 - - + +
75A GLY* 1.3 79.7 - - - +
77A LYS* 1.3 60.6 + - - +
87A VAL* 3.2 7.1 - - - +
88A GLY* 2.9 50.8 + - - +
89A VAL 4.7 0.2 - - - +
90A VAL* 4.9 9.2 - - + -
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Residues in contact with LYS 77 (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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18A PHE* 3.8 6.7 - - - -
42A VAL* 3.3 4.3 - - - -
43A GLU* 2.7 74.3 + - + +
44A THR 4.1 8.3 - - - -
45A ILE* 3.8 14.0 - - + +
46A LYS* 5.6 7.7 - - - +
76A VAL* 1.3 75.4 - - - +
78A CYS* 1.3 64.4 + - - +
79A THR* 4.7 8.1 + - - +
82A TYR* 3.7 59.0 - - + +
86A MET 3.4 8.1 - - - +
87A VAL* 4.2 1.3 - - + -
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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