Contacts of the strand formed by residues 84 - 90 (chain A) in PDB entry 3Q2P
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 ARG 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A PHE* 3.0 35.6 - - - -
15A LEU* 3.0 28.9 - - - +
18A PHE* 3.7 40.5 - - + -
75A ILE* 4.4 1.6 - - + -
76A SER 3.2 11.7 - - - +
77A GLU* 2.9 36.1 + - + +
82A ARG* 4.1 10.7 + - - +
83A GLY* 1.3 78.6 - - - +
85A LYS* 1.3 65.7 + - - +
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Residues in contact with LYS 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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18A PHE* 4.1 10.1 - - - -
22A GLU* 5.5 1.6 - - - -
75A ILE* 3.4 3.8 - - - +
76A SER* 2.9 54.4 + - - +
83A GLY 5.7 0.7 - - - +
84A ARG* 1.3 77.1 - - - +
86A LEU* 1.3 66.1 + - - +
87A LEU* 3.5 15.3 + - + +
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Residues in contact with LEU 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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18A PHE* 4.1 5.7 - - + -
19A ALA* 3.7 42.8 - - + +
22A GLU* 3.7 29.5 + - + +
23A GLU* 3.6 27.6 - - + +
26A ILE* 3.9 14.8 - - + +
73A ALA* 4.1 5.8 - - + -
74A ASP 3.9 7.9 - - - +
75A ILE* 4.4 4.0 - - + +
85A LYS* 1.3 73.4 - - - +
87A LEU* 1.3 63.6 + - - +
88A ARG 3.7 24.2 - - - +
89A PHE* 4.1 6.1 - - + -
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Residues in contact with LEU 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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59A GLU* 3.9 25.4 - - + +
74A ASP* 2.8 24.7 + - + +
75A ILE 4.0 2.5 - - - -
76A SER* 3.8 42.6 - - - +
85A LYS* 4.2 19.1 - - + +
86A LEU* 1.3 78.9 - - - +
88A ARG* 1.3 85.7 + - - +
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Residues in contact with ARG 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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59A GLU* 5.0 6.3 + - - -
72A ARG 4.3 1.1 - - - +
73A ALA* 3.2 4.0 - - - -
74A ASP* 2.8 64.8 + - + +
86A LEU* 3.7 7.9 - - - +
87A LEU* 1.3 105.7 + - - +
89A PHE* 1.3 61.7 + - - +
90A ASN* 3.9 19.3 - - - +
94B PRO* 3.9 39.4 + - - +
95B PRO 4.7 10.1 + - - -
96B PRO* 5.9 2.0 - - - +
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Residues in contact with PHE 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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19A ALA 4.0 25.8 - - - -
20A VAL* 4.6 9.0 - - + -
23A GLU* 3.1 33.2 - - + +
28A GLN* 5.1 3.1 + - - -
29A TYR* 3.5 27.1 + + - -
32A LEU* 3.7 26.5 - - + -
64A VAL* 4.1 20.2 - - + -
66A ALA* 5.2 0.2 - - + -
71A PHE* 3.4 40.6 - + + -
72A ARG 3.6 1.3 - - - -
73A ALA* 3.8 17.3 - - + -
86A LEU* 4.1 7.4 - - + -
88A ARG* 1.3 74.2 - - - +
90A ASN* 1.3 69.1 + - - +
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Residues in contact with ASN 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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29A TYR* 3.7 4.3 + - - -
71A PHE* 3.2 12.0 - - - +
72A ARG* 2.8 50.8 + - + +
74A ASP* 5.9 0.2 + - - -
88A ARG* 3.9 26.5 - - - +
89A PHE* 1.3 81.4 - - - +
91A GLY* 1.3 58.0 + - - +
93A VAL* 4.0 6.3 - - + +
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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