Contacts of the strand formed by residues 81 - 87 (chain A) in PDB entry 5HAN
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ALA* 4.5 4.0 - - + -
28A TYR 3.5 19.7 - - - +
29A ILE* 4.2 5.4 - - + -
39A PHE* 3.4 8.1 - - - -
74A GLU* 4.5 11.4 - - + +
75A VAL* 3.3 5.0 - - - -
76A ASP* 2.9 49.3 + - + +
79A ASN* 4.1 9.4 - - + +
80A SER* 1.3 76.2 - - - +
82A MET* 1.3 67.6 + - - +
83A LYS* 4.4 17.3 - - + +
353A TYR* 3.7 44.9 - - + +
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Residues in contact with MET 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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27A ALA* 3.7 0.5 - - - -
28A TYR* 2.8 58.8 + - + +
30A MET* 3.7 24.7 - - + -
39A PHE* 4.4 11.7 - - + -
43A ALA* 3.5 37.9 - - + -
46A PHE* 3.6 39.7 - - + -
72A VAL* 4.7 3.6 - - + -
74A GLU 3.7 4.9 - - - -
75A VAL* 4.5 1.3 - - + -
81A LEU* 1.3 74.0 - - - +
83A LYS* 1.4 63.7 + - - +
84A ILE* 4.0 18.4 - - + -
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Residues in contact with LYS 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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14A GLU* 2.9 32.7 + - - +
26A CYS 3.3 4.5 - - - +
27A ALA* 4.1 13.0 - - + -
72A VAL* 3.6 5.2 - - - +
73A TYR* 3.1 43.9 + - + +
74A GLU* 2.9 50.7 + - + +
81A LEU* 4.4 11.4 - - + +
82A MET* 1.4 76.9 - - - +
84A ILE* 1.3 61.9 + - - +
353A TYR* 3.9 40.1 + - - +
354A PHE* 4.5 2.0 - - + -
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Residues in contact with ILE 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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24A VAL 3.8 0.9 - - - +
25A LEU* 3.4 3.5 - - - -
26A CYS 2.9 31.8 + - - -
28A TYR* 3.8 16.4 - - + -
43A ALA 4.5 1.1 - - - +
46A PHE* 3.5 33.2 - - + -
47A ALA* 4.3 14.6 - - + +
70A ALA* 3.8 19.3 - - + -
71A LEU 3.4 11.7 - - - +
72A VAL* 4.1 10.8 - - + -
73A TYR* 3.6 3.8 - - - -
82A MET* 4.0 18.8 - - + -
83A LYS* 1.3 78.6 - - - +
85A ALA* 1.4 61.8 + - - +
86A TYR* 3.5 30.1 - - + +
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Residues in contact with ALA 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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12A LEU* 5.5 1.6 - - + -
17A LEU* 4.1 11.7 - - + -
23A HIS* 3.8 17.8 - - + -
24A VAL 3.5 5.2 - - - -
25A LEU* 3.7 20.0 - - + -
70A ALA* 3.1 4.5 - - - -
71A LEU* 2.8 43.3 + - + +
73A TYR* 3.6 12.7 - - + -
84A ILE* 1.4 71.4 - - - +
86A TYR* 1.3 60.5 + - - +
87A PRO* 3.7 3.6 - - - +
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Residues in contact with TYR 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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23A HIS* 3.4 3.2 - - - -
24A VAL* 2.7 42.8 + - + +
26A CYS* 3.8 20.2 - - - -
28A TYR* 2.8 29.9 + - - -
46A PHE* 4.4 0.3 - - - -
50A SER* 3.3 45.0 + - - -
70A ALA* 3.5 18.2 - - + -
84A ILE* 3.5 31.4 - - + +
85A ALA* 1.3 72.1 - - - +
87A PRO* 1.4 70.1 - - + +
88A ILE* 3.2 0.5 + - - -
90A LEU* 4.3 8.3 - - + -
91A PHE* 3.7 23.6 - + + -
108A LEU* 4.4 2.2 - - + -
109A THR* 3.8 18.0 - - + -
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Residues in contact with PRO 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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22A ARG 3.6 9.0 - - - +
23A HIS* 3.6 17.2 - - + +
67A GLY 4.4 5.8 - - - +
68A VAL* 3.6 31.0 - - + +
69A ASP 3.2 29.6 - - - +
71A LEU* 6.4 0.2 - - + -
85A ALA 3.7 4.9 - - - +
86A TYR* 1.4 81.3 - - - +
88A ILE* 1.3 65.1 + - - +
89A GLU* 3.1 15.0 - - - +
90A LEU* 3.1 26.0 + - + +
91A PHE* 3.9 2.6 - - - -
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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