Contacts of the strand formed by residues 75 - 85 (chain A) in PDB entry 4ZHF
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 LYS 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A LEU 3.5 0.3 - - - +
71A PHE* 3.5 4.9 - - - -
72A ARG 3.0 33.0 + - - +
73A LYS* 3.9 8.3 - - + +
74A LYS* 1.3 84.0 - - + +
76A CYS* 1.3 62.4 + - - +
77A ASP* 3.7 0.6 + - - -
175A CYS* 4.0 5.2 - - - -
6B ASP* 3.9 33.8 + - + +
7B LEU 3.4 18.8 - - - +
8B ILE* 4.6 16.8 - - + +
9B PRO* 4.0 2.2 - - - -
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Residues in contact with CYS 76 (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* 4.6 1.1 - - + -
70A LEU 3.4 1.1 - - - -
75A LYS* 1.3 70.6 - - - +
77A ASP* 1.3 60.4 + - - +
78A TYR* 3.6 31.1 - - + +
175A CYS* 2.1 54.7 - - + -
6B ASP* 3.2 9.3 - - - -
7B LEU* 2.8 34.8 + - + +
8B ILE 4.7 0.7 - - - -
9B PRO* 3.6 23.6 - - - -
10B ALA 5.0 0.9 - - - -
131B GLU* 5.7 4.3 - - - -
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Residues in contact with ASP 77 (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 SER 3.5 1.0 - - - +
69A VAL* 3.4 5.7 - - - -
70A LEU* 2.8 49.2 + - + +
72A ARG* 3.4 38.2 - - + -
75A LYS 4.7 0.2 - - - +
76A CYS* 1.3 75.4 - - - +
78A TYR* 1.3 76.5 + - - +
79A TRP* 5.3 1.4 + - - +
202A 4OL 5.3 8.1 - - - +
6B ASP* 3.3 21.7 - - - +
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Residues in contact with TYR 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A THR* 4.4 14.1 - - + -
68A SER 3.3 4.0 - - - +
69A VAL* 3.7 31.7 - - + +
76A CYS* 3.6 37.1 - - + +
77A ASP* 1.3 87.0 + - - +
79A TRP* 1.3 58.7 + - - +
80A ILE* 4.1 10.1 + - + +
175A CYS 5.2 1.2 + - - -
4B THR 4.9 10.5 + - - +
5B SER 4.4 4.9 - - - -
6B ASP* 4.6 1.4 + - - -
7B LEU* 4.3 12.4 - - + +
129B ASN* 3.4 22.5 + - + -
130B ARG* 3.8 38.8 - - + +
131B GLU* 3.4 26.3 + - - +
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Residues in contact with TRP 79 (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 THR* 3.4 0.5 - - - -
68A SER* 2.9 40.1 + - - +
70A LEU* 5.3 2.8 - - + +
77A ASP* 5.2 2.2 - - - +
78A TYR* 1.3 71.0 - - - +
80A ILE* 1.3 74.2 + - - +
81A ARG* 3.1 63.2 + - + +
94A LEU* 5.0 2.9 - - + -
100A TYR* 4.4 9.7 - + - -
106A TYR* 4.4 11.7 - + - -
202A 4OL 3.3 120.9 - + + -
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Residues in contact with ILE 80 (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 ASN* 4.8 13.5 - - + +
66A VAL 3.3 8.3 - - - +
67A THR* 3.9 26.0 - - + +
78A TYR* 4.1 10.5 + - + +
79A TRP* 1.3 88.1 + - - +
81A ARG* 1.3 72.8 + - - +
100A TYR* 4.4 2.8 + - - -
4B THR* 5.3 14.6 - - + -
128B GLN 5.8 3.1 - - - +
130B ARG* 6.6 0.2 - - - -
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Residues in contact with ARG 81 (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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54A THR* 4.0 0.2 - - - +
65A ASN* 3.7 5.6 + - - -
66A VAL* 2.8 64.1 + - - +
68A SER* 3.1 25.9 + - - +
79A TRP* 3.1 59.7 + - + -
80A ILE* 1.3 80.2 - - - +
82A THR* 1.3 61.3 + - - +
83A PHE* 3.9 16.0 - - + -
94A LEU* 3.7 20.4 - - + -
100A TYR* 3.5 20.0 - - - +
106A TYR* 5.6 0.6 + - - -
202A 4OL 3.7 0.6 - - - -
203A SO4 3.2 35.8 + - - -
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Residues in contact with THR 82 (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 LYS* 4.4 11.6 + - - +
63A SER* 4.2 14.1 - - - -
64A TYR 3.3 10.1 - - - +
65A ASN* 3.4 15.9 + - - -
81A ARG* 1.3 74.8 - - - +
83A PHE* 1.3 70.1 + - - +
84A VAL* 4.1 19.5 - - + -
94A LEU* 3.5 5.1 - - - +
95A GLY* 2.9 36.3 + - - +
96A ASN* 6.3 0.4 - - - -
100A TYR* 5.0 1.0 + - - -
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Residues in contact with PHE 83 (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 TYR* 3.8 31.6 - + - -
63A SER* 3.4 5.5 - - - -
64A TYR* 2.9 45.2 + + + -
66A VAL* 3.7 17.5 - - + -
81A ARG* 3.9 34.7 + - + -
82A THR* 1.3 78.9 - - - +
84A VAL* 1.3 61.2 + - - +
85A PRO* 4.0 0.5 - - - +
92A PHE* 3.9 24.5 - + + -
93A THR 3.5 4.9 - - - -
94A LEU* 4.0 10.8 - - + -
106A TYR* 4.4 6.7 - + - -
108A VAL* 3.8 38.6 - - + -
123A PHE* 4.0 12.1 - + - -
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Residues in contact with VAL 84 (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 SER* 3.7 11.0 - - - +
82A THR* 4.1 8.3 - - + -
83A PHE* 1.3 72.8 - - - +
85A PRO* 1.3 86.1 - - + +
92A PHE* 3.1 3.9 - - - -
93A THR* 2.7 47.0 + - - +
94A LEU 4.6 0.4 - - - +
95A GLY* 3.8 26.9 - - - -
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Residues in contact with PRO 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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61A ASP 5.0 2.0 - - - +
62A LYS* 3.4 31.9 - - + +
63A SER* 3.4 17.7 - - - +
83A PHE 4.0 0.7 - - - +
84A VAL* 1.3 99.1 - - + +
86A GLY* 1.3 63.0 - - - +
91A GLU 3.7 7.6 - - - +
92A PHE* 3.7 11.4 - - + -
93A THR* 5.1 1.2 + - - -
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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