Contacts of the strand formed by residues 63 - 72 (chain A) in PDB entry 4D85
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 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A THR 3.4 3.3 + - - +
62A TYR* 1.3 84.8 - - - +
64A ASP* 1.3 64.9 + - - +
65A LEU* 4.5 1.3 - - + +
83A GLY* 3.1 3.3 - - - -
84A THR* 2.8 49.5 + - - +
98A ARG* 3.3 47.5 - - - +
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Residues in contact with ASP 64 (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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56A ARG* 5.4 1.6 + - - -
62A TYR* 3.3 31.5 + - + +
63A ARG* 1.3 78.9 - - - +
65A LEU* 1.3 67.0 + - - +
66A ARG* 2.5 52.6 + - + +
81A GLU* 5.6 3.8 - - - +
82A LEU 3.7 4.4 - - - +
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Residues in contact with LEU 65 (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* 5.2 1.1 - - + +
64A ASP* 1.3 82.8 + - - +
66A ARG* 1.3 63.7 + - - +
67A LYS* 3.0 18.4 + - + +
82A LEU* 2.9 27.2 + - + +
83A GLY* 3.3 37.5 - - - +
84A THR* 3.6 12.3 - - + +
100A ASN* 3.4 20.0 - - - +
135A LEU* 4.9 5.2 - - + -
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Residues in contact with ARG 66 (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 ASP* 2.5 35.7 + - + +
65A LEU* 1.3 74.6 - - - +
67A LYS* 1.3 56.8 + - - +
82A LEU 3.9 1.6 + - - -
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Residues in contact with LYS 67 (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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65A LEU* 3.0 12.3 + - + +
66A ARG* 1.3 80.9 - - - +
68A GLY* 1.3 76.1 + - - +
81A GLU* 4.0 2.1 - - - +
82A LEU* 3.1 46.6 + - + +
131A PRO* 4.4 16.0 - - + +
132A ASP* 5.4 3.8 + - - -
134A SER* 4.5 14.6 + - - -
135A LEU* 5.9 4.9 - - - +
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Residues in contact with GLY 68 (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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67A LYS* 1.3 92.0 - - - +
69A VAL* 1.3 64.3 + - - +
80A GLY 3.7 9.6 - - - -
81A GLU* 4.9 1.8 - - - -
82A LEU* 3.7 0.7 - - - +
131A PRO* 3.5 9.5 - - - +
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Residues in contact with VAL 69 (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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39A ASN* 4.2 9.4 - - - +
68A GLY* 1.3 73.5 - - - +
70A TYR* 1.3 65.5 + - - +
78A TRP* 4.1 19.7 - - + -
79A GLU* 3.3 6.0 - - - +
80A GLY 3.0 45.5 + - - +
81A GLU 4.4 0.4 - - - +
82A LEU* 3.4 34.3 - - + -
102A ALA* 4.3 4.5 - - + -
130A ARG* 3.7 35.0 - - + +
131A PRO* 3.9 5.2 - - + -
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Residues in contact with TYR 70 (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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69A VAL* 1.3 77.9 - - - +
71A VAL* 1.3 65.0 + - - +
72A PRO* 3.5 36.5 - - + +
77A LYS* 3.8 27.3 + - + +
78A TRP 3.3 20.6 - - - -
79A GLU* 4.1 17.3 - - + -
130A ARG* 3.5 18.8 - - - +
131A PRO* 5.4 1.2 - - - +
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Residues in contact with VAL 71 (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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39A ASN* 3.8 11.2 - - + +
69A VAL* 4.3 1.3 - - + -
70A TYR* 1.3 80.9 - - - +
72A PRO* 1.3 62.2 - - - +
73A TYR* 3.6 30.6 + - + +
77A LYS* 3.5 2.4 - - - -
78A TRP* 3.1 65.0 + - + -
130A ARG* 3.5 22.9 - - + -
401A 0GU 3.8 27.6 - - + -
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Residues in contact with PRO 72 (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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70A TYR* 3.5 39.5 - - + +
71A VAL* 1.3 86.8 - - + +
73A TYR* 1.3 65.3 + - - +
77A LYS* 3.8 20.4 - - + -
130A ARG* 5.0 7.4 - - - +
401A 0GU 3.6 24.0 - - + +
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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