Contacts of the strand formed by residues 84 - 89 (chain A) in PDB entry 3O4P
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 GLN 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A CYS* 3.7 2.3 - - - -
79A ASP* 2.9 57.5 + - + +
82A ALA* 3.0 19.0 + - + +
83A ASN* 1.3 75.3 - - - +
85A LEU* 1.3 65.6 + - - +
86A PHE* 4.0 4.6 - - + -
96A VAL* 3.4 16.4 - - + +
97A VAL 3.5 7.9 - - - +
98A GLN* 2.9 36.9 + - - +
99A THR* 5.5 1.1 - - - +
461A PEG 3.4 29.3 - - - +
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Residues in contact with LEU 85 (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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24A VAL* 4.1 19.5 - - + -
26A ASP* 4.6 11.9 - - + -
32A TYR* 3.9 38.1 - - + -
48A ILE* 4.7 13.7 - - + -
61A ILE* 5.5 1.8 - - + -
76A CYS* 5.0 3.4 - - + -
77A GLN 3.5 2.7 - - - +
78A CYS* 4.0 30.7 - - + -
83A ASN 6.1 0.2 - - - -
84A GLN* 1.3 75.9 - - - +
86A PHE* 1.3 64.3 + - - +
87A VAL* 3.9 16.2 + - + -
95A LEU 3.7 0.2 - - - +
96A VAL* 3.3 4.9 - - - +
97A VAL* 2.8 48.5 + - + +
98A GLN 6.3 0.4 - - - -
99A THR* 6.3 2.9 - - + -
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Residues in contact with PHE 86 (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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75A GLY 3.8 0.3 - - - +
76A CYS* 3.2 5.7 - - - +
77A GLN 2.8 37.3 + - - +
79A ASP* 3.8 30.1 - - + -
84A GLN* 4.0 7.4 - - + -
85A LEU* 1.3 74.1 - - - +
87A VAL* 1.3 61.3 + - - +
88A ALA 4.2 0.4 - - - -
94A LEU* 4.1 4.7 - - + -
95A LEU 3.4 3.8 - - - -
96A VAL* 3.3 28.9 - - + -
106A ILE* 3.9 13.0 - - + -
122A CYS* 3.9 4.8 - - - -
124A PHE* 3.7 19.3 - + + -
130A LEU* 3.8 29.4 - - + -
158A PHE* 4.3 4.0 - + - -
422A EDO 3.1 35.0 - - - -
461A PEG 3.9 15.0 - - - -
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Residues in contact with VAL 87 (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 VAL* 4.5 1.3 - - + -
48A ILE* 4.3 11.7 - - + -
73A PRO* 3.7 30.3 - - + -
75A GLY 3.2 9.9 - - - +
76A CYS* 4.0 19.3 - - - -
85A LEU* 4.0 14.4 - - + -
86A PHE* 1.3 80.7 - - - +
88A ALA* 1.3 66.1 + - - +
89A ASP 3.6 0.5 + - - -
94A LEU* 3.5 6.3 - - - +
95A LEU* 2.8 52.4 + - + +
97A VAL* 3.8 22.0 - - + -
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Residues in contact with ALA 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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73A PRO* 3.7 1.2 - - - +
74A ALA* 2.8 32.1 + - - -
75A GLY 2.8 12.8 + - - +
86A PHE 4.2 0.4 - - - -
87A VAL* 1.3 71.0 - - - +
89A ASP* 1.3 54.6 + - - +
93A GLY 3.6 5.6 - - - -
94A LEU* 4.3 4.3 - - + +
119A CYS* 3.6 15.4 - - + +
120A ASN 3.5 29.6 - - - +
121A ASP* 3.6 14.6 - - - +
122A CYS* 4.6 5.5 - - - -
132A ILE* 4.7 2.7 - - + -
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Residues in contact with ASP 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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64A PRO* 4.1 0.9 - - - +
71A GLY* 3.3 9.4 - - - -
72A ILE 2.9 30.9 + - - -
73A PRO* 3.2 15.6 - - + +
87A VAL 5.0 0.2 - - - -
88A ALA* 1.3 73.7 - - - +
90A MET* 1.3 58.8 + - - +
91A ARG* 2.8 27.5 + - - -
92A LEU* 2.9 22.4 + - + +
93A GLY 2.8 35.8 + - - +
95A LEU* 3.8 22.6 - - + +
119A CYS 2.9 14.3 + - - -
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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