Contacts of the strand formed by residues 90 - 97 (chain A) in PDB entry 2ZJP
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 ALA 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A TYR* 4.4 5.6 - - - -
85A ASP 3.9 22.3 + - - +
88A ARG* 3.3 22.9 - - + +
89A SER* 1.3 80.1 - - - +
91A ARG* 1.3 66.3 + - - +
92A ILE* 4.3 3.8 - - - +
106A LEU* 5.6 3.1 - - + -
107A ALA 5.7 1.1 - - - +
157A ARG 4.6 11.2 - - - +
159A ALA* 4.8 5.6 - - + +
196A VAL* 5.5 6.5 - - + -
198A ASN* 2.9 20.8 - - + +
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Residues in contact with ARG 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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82A ILE* 3.3 35.0 - - + +
83A GLU 3.8 5.2 - - - +
84A TYR* 5.2 2.7 - - + +
90A ALA* 1.3 80.1 - - - +
92A ILE* 1.3 62.2 + - - +
106A LEU* 3.8 3.6 - - - +
107A ALA* 2.9 39.4 + - + +
108A PRO 4.8 6.9 + - - -
109A GLU* 5.1 11.2 + - - -
110A GLY 5.8 1.8 - - - +
111A LEU 5.1 5.7 + - - -
198A ASN* 3.0 35.2 + - + +
199A ALA* 4.4 14.3 - - - +
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Residues in contact with ILE 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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63A ARG* 4.5 6.1 - - + -
65A ILE* 3.9 23.8 - - + -
81A ALA 3.5 2.1 - - - +
82A ILE* 3.5 2.1 - - - -
83A GLU* 3.0 34.4 + - + +
85A ASP* 2.8 42.2 - - + +
88A ARG* 4.6 13.5 - - - +
90A ALA 4.3 6.7 - - - +
91A ARG* 1.3 79.3 - - - +
93A ALA* 1.3 60.4 + - - +
94A LEU 3.8 0.2 + - - -
104A TYR* 3.3 42.7 - - + -
105A ILE 3.7 11.4 - - - +
106A LEU* 5.2 2.7 - - + -
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Residues in contact with ALA 93 (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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79A VAL* 4.4 15.5 - - + -
81A ALA 3.3 5.8 - - - +
82A ILE* 4.0 15.0 - - + +
92A ILE* 1.3 73.4 - - - +
94A LEU* 1.3 59.0 + - - +
95A LEU* 3.4 15.5 + - + +
105A ILE* 2.8 39.9 + - - +
106A LEU 5.3 0.4 - - - +
107A ALA* 3.7 22.7 - - + +
111A LEU* 5.9 3.1 - - + -
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Residues in contact with LEU 94 (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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34A THR* 5.8 5.6 - - + -
80A ALA* 2.9 35.0 - - + +
81A ALA* 3.0 16.8 + - + +
83A GLU* 5.8 0.7 - - + +
92A ILE 3.8 0.2 + - - -
93A ALA* 1.3 71.0 - - - +
95A LEU* 1.3 71.9 + - - +
96A HIS* 4.9 0.6 - - + +
102A LYS* 3.6 40.4 - - + +
103A ARG 3.8 0.2 - - - -
104A TYR* 3.7 52.3 - - + +
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Residues in contact with LEU 95 (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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77A ALA* 3.9 13.2 - - + -
78A LYS 3.2 6.7 - - - -
79A VAL* 3.7 38.1 - - + +
93A ALA* 3.4 17.0 + - + +
94A LEU* 1.3 91.7 - - - +
96A HIS* 1.3 60.6 + - - +
97A TYR* 5.2 5.3 - - + +
102A LYS* 4.2 6.8 - - - +
103A ARG 4.3 6.5 + - - +
105A ILE* 3.4 40.8 - - + -
111A LEU* 6.0 1.8 - - + -
117A VAL* 3.7 39.9 - - + -
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Residues in contact with HIS 96 (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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77A ALA* 2.9 22.9 - - - +
78A LYS* 3.3 13.0 + - + +
80A ALA* 5.8 3.1 - - + -
94A LEU 4.9 1.8 - - - +
95A LEU* 1.3 78.0 - - - +
97A TYR* 1.3 88.0 + - - +
98A ALA* 3.9 1.0 + - - -
100A GLY* 2.9 32.9 + - - -
101A GLU 3.3 10.7 + - - -
102A LYS* 3.5 17.4 - - + +
1516X A 4.0 0.4 - - - -
1517X C 2.7 62.1 + - - +
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Residues in contact with TYR 97 (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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66A ASP* 4.3 12.0 + - - +
69A ARG* 4.6 8.4 + - - -
72A LYS* 3.3 44.4 - - + +
75A VAL* 3.4 26.5 - - + -
76A ASN 3.3 7.0 - - - -
77A ALA* 3.5 20.2 - - + -
95A LEU* 5.2 5.2 - - + -
96A HIS* 1.3 109.2 + - - +
98A ALA* 1.3 53.5 + - - +
99A ASP* 2.8 23.8 + - + +
100A GLY 3.2 0.5 + - - -
101A GLU* 4.0 16.7 + - + +
103A ARG* 4.5 22.3 - - + +
105A ILE* 3.0 32.0 - - + +
117A VAL* 6.2 2.9 - - + -
118A ASN 6.6 0.4 - - - -
119A ALA* 5.9 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