Contacts of the strand formed by residues 98 - 104 (chain A) in PDB entry 1ZGA
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 GLU 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A ILE* 3.8 34.7 - - + +
89A VAL 3.6 4.0 - - - +
90A LYS* 4.6 18.6 - - + +
96A GLU 4.0 2.8 - - - +
97A GLU* 1.3 90.3 - - + +
99A GLU* 1.3 66.2 + - - +
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Residues in contact with GLU 99 (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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53A THR* 3.5 31.8 + - + -
54A LEU* 4.9 2.3 + - - +
55A SER* 3.8 11.0 + - - -
88A ILE* 3.5 5.9 - - - -
89A VAL* 2.7 43.0 + - - +
91A GLY* 4.1 8.1 - - - +
92A LYS* 5.5 2.3 - - - +
96A GLU* 2.9 40.9 - - - +
98A GLU* 1.3 79.2 - - - +
100A ILE* 1.3 67.5 + - - +
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Residues in contact with ILE 100 (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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53A THR* 3.4 21.9 - - - -
54A LEU 4.1 4.0 + - - -
72A HIS* 5.1 10.5 - - + +
86A LYS* 3.7 44.0 - - + +
87A THR 3.3 8.1 - - - +
88A ILE* 4.5 13.9 - - + -
99A GLU* 1.3 74.6 - - - +
101A ALA* 1.3 66.0 + - - +
102A TYR* 3.8 27.2 - - + +
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Residues in contact with ALA 101 (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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51A PRO* 3.5 28.0 - - + +
52A MET 3.2 10.8 - - - +
53A THR* 4.5 3.8 - - + +
85A ALA 3.4 4.2 - - - +
86A LYS* 3.6 2.6 - - - -
87A THR* 2.6 37.8 + - + +
89A VAL* 3.6 25.8 - - + -
100A ILE* 1.3 75.0 - - - +
102A TYR* 1.3 63.8 + - - +
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Residues in contact with TYR 102 (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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45A ILE* 3.6 25.9 - - + +
51A PRO* 3.4 2.6 - - - +
52A MET 2.6 40.0 + - - +
53A THR 4.6 0.9 - - - -
54A LEU* 4.2 21.9 - - + +
57A LEU* 5.0 5.4 - - + -
72A HIS* 3.8 25.5 + - - -
75A LEU* 3.7 40.0 - - + +
76A ARG 5.3 0.2 + - - -
79A THR* 3.7 25.1 - - - -
84A PHE* 4.4 11.7 - - + -
85A ALA 3.6 3.4 - - - +
86A LYS* 4.1 24.9 - - + -
100A ILE* 3.8 25.2 - - + +
101A ALA* 1.3 73.4 - - - +
103A SER* 1.3 61.9 + - - +
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Residues in contact with SER 103 (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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45A ILE* 4.4 5.8 - - - -
51A PRO* 3.5 29.0 - - - +
84A PHE* 3.2 9.9 - - - +
85A ALA* 2.9 43.6 + - - -
87A THR* 4.8 6.4 + - - -
102A TYR* 1.3 72.3 - - - +
104A LEU* 1.3 68.8 + - - +
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Residues in contact with LEU 104 (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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42A ALA* 3.5 40.4 - - + +
45A ILE* 3.7 28.3 - - + +
46A HIS* 4.0 12.1 - - + +
83A PHE 4.4 0.9 - - - -
84A PHE* 4.0 8.5 - - + -
85A ALA* 4.9 1.7 - - - +
103A SER* 1.3 81.8 - - - +
105A THR* 1.3 63.7 + - - +
108A SER* 3.4 17.5 - - - +
109A LYS* 4.0 26.7 + - + -
112A ILE* 3.9 27.6 - - + -
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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