Contacts of the strand formed by residues 68 - 74 (chain A) in PDB entry 3WUZ
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 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ASP 3.5 0.6 + - - -
67A VAL* 1.3 73.9 - - - +
69A ILE* 1.3 63.3 + - - +
70A SER* 3.8 11.3 + - - +
83A SER* 3.1 28.3 + - - +
84A THR* 3.7 3.1 - - - -
85A ARG* 3.0 33.5 + - + +
86A PRO* 3.9 13.9 + - - +
126A ARG* 3.7 1.6 - - - +
127A VAL* 3.7 2.3 - - - -
128A GLU* 2.8 49.9 + - + +
136A ARG* 4.0 15.5 - - - +
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Residues in contact with ILE 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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53A PHE* 3.9 23.1 - - + -
67A VAL* 4.0 14.1 - - + -
68A ARG* 1.3 76.9 - - - +
70A SER* 1.3 64.6 + - - +
71A TRP* 3.8 26.7 - - + +
82A TYR* 5.0 1.0 - - - -
83A SER* 3.3 2.8 + - - -
84A THR* 2.8 44.7 + - + +
99A LEU* 4.1 11.0 - - + -
101A TRP* 3.6 36.6 - - + +
125A CYS* 3.9 9.6 - - - -
126A ARG 3.3 5.6 - - - +
127A VAL* 4.2 13.0 - - + -
201A IPA 4.8 1.3 - - - +
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Residues in contact with SER 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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68A ARG* 3.8 15.4 + - - +
69A ILE* 1.3 71.5 - - - +
71A TRP* 1.3 67.6 + - - +
72A ARG* 5.2 2.7 - - - -
80A SER* 5.2 9.4 - - - -
82A TYR 3.3 11.2 - - - -
83A SER* 3.0 20.6 + - - -
124A PHE 3.7 0.2 - - - +
125A CYS* 3.6 3.3 - - - -
126A ARG* 2.8 52.2 + - - +
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Residues in contact with TRP 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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37A GLN* 4.1 8.5 - - - -
51A ILE* 3.6 40.4 - - + -
53A PHE* 3.7 21.8 - + + -
69A ILE* 3.8 14.9 - - + +
70A SER* 1.3 78.6 - - - +
72A ARG* 1.3 61.5 + - - +
80A SER* 3.5 3.6 - - - -
81A PHE* 2.9 45.5 + + + -
82A TYR* 2.9 32.0 + + + +
99A LEU* 3.7 17.6 - - - +
110A LEU* 3.6 32.0 - - + +
123A TYR* 4.4 9.0 - - + -
124A PHE 3.2 24.5 - - - -
125A CYS* 3.6 29.8 - - + -
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Residues in contact with ARG 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 SER* 5.2 2.7 - - - -
71A TRP* 1.3 80.2 - - - +
73A ARG* 1.3 62.1 + - - +
77A HIS 4.2 5.7 + - - -
78A GLY* 3.4 30.8 + - - -
79A GLN* 3.2 11.3 - - - +
80A SER* 3.0 39.0 + - - +
81A PHE* 3.6 7.0 - - - -
123A TYR* 3.3 3.8 - - - -
124A PHE* 2.8 43.4 + - + +
126A ARG* 3.5 33.5 - - - +
140A GLN* 3.3 29.1 + - - +
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Residues in contact with ARG 73 (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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72A ARG* 1.3 76.2 - - - +
74A GLY* 1.3 59.6 + - - +
78A GLY* 3.3 1.7 - - - -
79A GLN* 2.8 40.3 + - + +
81A PHE* 3.8 12.7 - - + -
93A TYR* 2.9 37.2 + - - -
118A GLN 2.9 28.7 + - - -
119A ASP* 3.9 5.1 + - - +
120A GLN 3.6 14.8 + - - -
121A SER* 3.5 19.9 + - - +
122A VAL 3.1 6.7 - - - +
123A TYR* 4.0 8.7 + - + -
124A PHE* 4.8 1.8 - - - -
202A CIT 2.9 30.0 + - + +
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Residues in contact with GLY 74 (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 ARG* 1.3 75.6 - - - +
75A HIS* 1.3 61.8 + - - +
77A HIS 5.0 0.2 - - - -
78A GLY* 3.9 8.1 - - - -
121A SER* 3.1 15.6 + - - -
122A VAL* 2.9 32.3 + - - +
124A PHE* 4.5 6.7 - - - -
202A CIT 3.4 17.3 - - - -
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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