Contacts of the strand formed by residues 66 - 73 (chain A) in PDB entry 2HZ5
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 LEU 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ILE* 4.4 9.4 - - + +
53A ALA* 4.0 10.1 - - + -
54A ARG* 3.9 46.0 + - + +
57A VAL* 3.6 13.9 - - + +
58A ARG* 6.1 0.4 - - - +
65A ASP* 1.3 75.4 - - - +
67A THR* 1.3 60.9 - - - +
68A PHE 3.9 13.2 - - - +
69A LEU* 4.1 15.9 - - + -
80A VAL* 6.1 0.4 - - + -
82A PRO* 3.7 30.0 - - + +
87A PHE* 5.3 0.2 - - + -
71B ILE* 3.4 32.5 - - + -
72B ARG 3.6 11.9 - - - +
73B SER* 4.2 3.1 - - - -
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Residues in contact with THR 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 ASP* 3.4 3.5 + - + +
66A LEU* 1.3 78.4 - - - +
68A PHE* 1.3 63.8 + - - +
81A ALA* 4.1 6.6 - - - +
82A PRO* 3.4 22.5 - - - +
72B ARG* 2.9 32.3 + - - +
73B SER* 3.5 4.0 + - - -
74B LYS* 3.6 46.9 - - + +
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Residues in contact with PHE 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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66A LEU* 3.9 6.2 - - - +
67A THR* 1.3 80.9 - - - +
69A LEU* 1.3 71.2 + - - +
70A ARG* 4.0 24.9 - - + -
79A MET* 3.5 43.1 - - + -
80A VAL 3.4 17.5 - - - -
81A ALA* 4.3 13.0 - - + -
82A PRO* 4.5 0.9 - - - -
70B ARG* 5.9 0.2 - - - -
71B ILE* 3.7 1.2 - - - -
72B ARG* 2.7 77.7 + - + +
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Residues in contact with LEU 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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49A PHE* 4.0 23.3 - - + -
50A ILE* 4.5 11.4 - - + -
53A ALA* 3.6 33.2 - - + -
66A LEU* 4.1 16.8 - - + -
68A PHE* 1.3 76.6 - - - +
70A ARG* 1.3 59.9 + - - +
71A ILE* 4.3 4.0 - - + -
78A ILE 3.8 0.6 - - - +
79A MET* 3.2 5.9 - - - +
80A VAL* 2.8 53.6 + - + +
49B PHE* 3.9 8.5 - - + -
69B LEU* 4.5 5.4 - - + -
70B ARG 3.4 6.7 - - - +
71B ILE* 3.9 28.7 - - + -
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Residues in contact with ARG 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 PHE* 4.0 20.4 - - + -
69A LEU* 1.3 76.2 - - - +
71A ILE* 1.3 61.7 + - - +
72A ARG* 3.6 35.1 - - - +
77A GLU* 2.9 35.5 + - + -
78A ILE 3.4 5.4 - - - +
79A MET* 3.4 32.2 - - + -
92A GLN* 3.6 3.6 + - - -
68B PHE* 4.0 0.9 - - - +
69B LEU* 3.4 6.6 - - - +
70B ARG* 2.9 54.1 + - + +
72B ARG* 6.0 1.8 - - - +
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Residues in contact with ILE 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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46A MET* 3.9 20.6 - - + -
49A PHE* 3.4 36.3 - - + -
69A LEU* 4.7 6.3 - - + -
70A ARG* 1.3 77.9 - - - +
72A ARG* 1.3 60.5 + - - +
73A SER* 4.1 0.5 + - - -
76A ASN* 5.3 0.3 - - - +
77A GLU* 3.3 2.5 - - - -
78A ILE* 2.8 60.2 + - + +
80A VAL* 4.4 7.6 - - + -
53B ALA* 5.0 2.5 - - + +
57B VAL* 3.8 20.0 - - + -
66B LEU* 3.5 27.1 - - + -
68B PHE 3.8 2.0 - - - -
69B LEU* 3.8 12.6 - - + -
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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 ARG* 3.6 26.8 - - - +
71A ILE* 1.3 73.9 - - - +
73A SER* 1.3 69.4 + - - +
76A ASN 3.9 4.5 - - - +
77A GLU* 3.2 33.6 + - + +
94A PRO* 5.1 8.5 - - + -
66B LEU* 3.6 7.0 - - - +
67B THR* 2.9 29.7 + - - +
68B PHE* 2.7 63.7 + - + +
70B ARG* 6.0 1.6 - - - +
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Residues in contact with SER 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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71A ILE 5.4 0.9 - - - -
72A ARG* 1.3 79.3 - - - +
74A LYS* 1.3 65.6 + - - +
76A ASN* 2.8 34.7 + - - +
94A PRO* 4.2 5.9 - - - +
57B VAL* 4.1 10.3 - - - -
64B ASN* 2.8 31.3 + - - -
65B ASP 3.1 20.4 - - - -
66B LEU* 4.2 1.1 - - - -
67B THR* 3.5 9.8 + - - -
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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