Contacts of the strand formed by residues 87 - 92 (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 VAL 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A VAL* 5.6 0.5 - - - +
18A PHE* 3.6 17.1 + - - +
21A ALA* 4.2 12.5 - - - +
45A ILE* 4.0 7.2 - - + -
76A VAL 3.2 13.7 - - - +
77A LYS* 4.2 0.7 - - + -
82A TYR* 3.8 19.5 - - + -
85A GLY 3.0 17.0 + - - +
86A MET* 1.3 78.8 - - - +
88A GLY* 1.3 59.9 + - - +
111A ALA* 3.6 43.5 - - + +
114A ARG* 3.8 15.2 - - + +
115A LEU* 3.7 17.9 - - + +
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Residues in contact with GLY 88 (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* 4.0 4.2 - - - -
21A ALA* 3.2 17.9 - - - -
75A GLY* 3.6 1.2 - - - -
76A VAL* 2.9 42.4 + - - +
87A VAL* 1.3 76.6 - - - +
89A VAL* 1.3 70.0 + - - +
115A LEU* 3.9 2.9 - - - +
118A ALA* 5.3 1.3 - - - -
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Residues in contact with VAL 89 (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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21A ALA 2.9 6.2 + - - +
22A SER* 3.5 3.5 + - - -
23A LEU* 3.2 22.2 + - - +
48A MET* 5.2 2.5 - - + -
73A VAL* 3.4 28.7 - - + -
74A TYR 3.4 3.8 - - - -
75A GLY* 4.6 5.8 - - - -
88A GLY* 1.3 80.3 - - - +
90A VAL* 1.3 68.0 + - - +
91A GLN 4.1 0.2 - - - -
115A LEU* 3.6 21.3 - - + -
118A ALA* 4.1 19.7 - - + -
119A LEU* 4.0 17.9 - - + -
122A LEU* 3.5 24.9 - - + -
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Residues in contact with VAL 90 (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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23A LEU* 3.4 19.3 - - + +
25A VAL* 4.2 17.9 - - + -
31A VAL* 4.6 2.7 - - + -
33A PHE* 4.4 17.3 - - + -
68A PHE* 4.0 36.8 - - + -
72A GLY 3.8 0.3 - - - +
73A VAL* 3.6 1.0 - - - -
74A TYR* 2.8 44.0 + - + +
76A VAL* 4.9 10.3 - - + -
89A VAL* 1.3 77.7 - - - +
91A GLN* 1.3 61.9 + - - +
92A VAL* 3.8 14.0 + - + -
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Residues in contact with GLN 91 (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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23A LEU 2.8 14.4 + - - +
24A LYS* 3.3 24.8 + - + +
25A VAL* 2.9 29.6 + - - +
72A GLY 3.8 3.8 - - - +
73A VAL* 4.1 10.0 - - + +
89A VAL* 4.1 1.6 - - - +
90A VAL* 1.3 71.2 - - - +
92A VAL* 1.3 61.1 + - - +
93A GLY 2.9 24.4 - - - +
94A ASP* 4.2 2.6 - - - -
95A ALA 4.4 0.3 + - - -
96A PRO* 3.5 31.9 - - + +
99A LEU* 5.5 2.0 - - - +
122A LEU* 3.7 42.1 + - + +
124A ASN* 5.2 3.6 + - - -
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Residues in contact with VAL 92 (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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25A VAL* 3.6 10.1 - - + -
26A ALA 4.0 4.9 - - - +
27A PRO* 3.6 31.0 - - + -
68A PHE* 3.5 35.0 - - + -
69A THR 4.7 0.7 - - - +
70A ALA 4.1 12.8 - - - +
71A PRO* 3.5 9.4 - - + +
72A GLY* 2.8 32.4 + - - +
74A TYR* 3.5 25.4 - - + -
90A VAL* 4.1 3.8 - - + -
91A GLN* 1.3 73.8 - - - +
93A GLY* 1.3 64.2 + - - +
94A ASP 5.1 0.3 - - - +
96A PRO* 5.5 0.7 - - - +
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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