Contacts of the strand formed by residues 76 - 85 (chain A) in PDB entry 5I2S
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 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A CYS* 3.6 17.5 - - - -
69A ASP 3.4 6.7 - - - +
70A PHE* 3.4 48.8 - - + +
74A GLY 3.4 2.6 + - - +
75A PRO* 1.3 75.2 - - - +
77A TYR* 1.3 64.3 + - - +
78A ILE* 4.0 25.7 + - + +
112A GLN* 5.3 6.5 - - - +
114A CYS* 3.8 17.3 - - - -
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Residues in contact with TYR 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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67A THR* 3.8 1.9 - - - +
69A ASP* 2.9 45.2 + - + +
71A ARG* 3.9 39.3 - - + +
73A TYR* 5.2 6.5 - + - -
75A PRO* 3.7 33.9 - - + +
76A LYS* 1.3 73.0 - - - +
78A ILE* 1.3 60.6 + - - +
79A THR* 3.9 8.9 + - + +
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Residues in contact with ILE 78 (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 THR* 4.4 7.0 - - + -
67A THR 3.1 16.8 - - - +
68A CYS* 4.5 10.1 - - - -
76A LYS* 4.0 31.3 + - + +
77A TYR* 1.3 74.2 - - - +
79A THR* 1.3 63.4 + - - +
80A HIS* 4.3 21.0 - - + +
112A GLN* 3.2 28.9 - - + +
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Residues in contact with THR 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* 2.9 48.5 + - - +
77A TYR* 3.9 7.6 + - + +
78A ILE* 1.3 78.6 - - - +
80A HIS* 1.3 67.5 + - - +
81A SER* 4.2 1.8 - - - -
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Residues in contact with HIS 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 VAL 3.4 3.1 - - - -
66A THR* 3.3 36.0 + - + +
78A ILE* 4.3 13.5 - - + +
79A THR* 1.3 97.0 - - - +
81A SER* 1.3 59.7 + - - +
82A ILE* 4.2 1.7 + - - +
109A PHE* 3.9 47.1 - + + -
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Residues in contact with SER 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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64A TRP* 4.0 0.2 - - - -
65A VAL* 2.9 45.8 + - - +
67A THR* 5.0 3.7 + - - -
79A THR* 4.2 1.3 - - - -
80A HIS* 1.3 75.2 - - - +
82A ILE* 1.3 65.3 + - - +
83A ARG* 3.4 29.9 + - - -
109A PHE* 4.8 0.2 - - - -
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Residues in contact with ILE 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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62A SER* 3.9 5.2 - - - -
63A LYS 3.6 1.3 - - - -
64A TRP* 3.5 52.3 - - + +
80A HIS 5.2 1.3 - - - +
81A SER* 1.3 74.8 - - - +
83A ARG* 1.3 67.7 + - - +
84A SER 4.1 0.6 + - - -
109A PHE* 3.5 26.7 - - + -
409A HIS* 3.4 37.0 - - + +
410A ILE* 6.3 0.4 - - + -
413A ALA* 5.1 14.4 - - + -
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Residues in contact with ARG 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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62A SER* 4.4 0.4 - - - -
63A LYS* 2.9 43.4 + - + +
65A VAL* 4.2 19.0 - - + +
67A THR* 5.7 1.8 + - - -
81A SER* 3.4 24.3 + - - +
82A ILE* 1.3 80.4 - - - +
84A SER* 1.3 68.3 + - - +
85A PHE* 4.5 1.0 - - - +
121A ASP* 4.8 12.1 + - - -
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Residues in contact with SER 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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61A ALA 3.4 13.8 + - - -
62A SER* 3.8 6.6 - - - +
82A ILE 4.1 1.2 - - - -
83A ARG* 1.3 79.3 - - - +
85A PHE* 1.3 65.5 + - - +
164A SER* 3.6 19.8 + - - -
407A HIS* 3.8 23.0 + - - -
409A HIS* 4.0 21.1 + - - -
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Residues in contact with PHE 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 ALA* 2.8 50.4 + - + +
62A SER 4.2 4.9 - - - -
63A LYS* 3.9 35.0 - - + -
83A ARG 4.5 1.1 - - - +
84A SER* 1.3 83.6 + - - +
86A THR* 1.3 83.0 + - - +
87A PRO* 3.5 7.8 - - + +
88A SER 5.3 0.2 - - - -
91A GLN* 4.2 20.6 - - - -
125A VAL* 3.9 32.3 - - + -
127A VAL* 5.1 0.9 - - + -
164A SER* 4.3 5.0 + - - -
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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