Contacts of the strand formed by residues 64 - 71 (chain B) in PDB entry 5I73
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 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B VAL* 3.8 12.8 - - + -
57B LYS 3.8 1.8 - - - -
58B GLN* 3.5 39.7 - - + +
63B SER* 1.3 83.2 + - - +
65B GLU* 1.3 60.8 + - - +
114B TYR* 5.1 1.8 - - + -
128B TRP* 3.9 17.7 - - + -
56C TYR* 5.5 2.0 - - + -
58C GLN* 4.3 0.4 - - - +
64C PRO* 3.9 24.5 - - + -
107C TYR* 4.4 22.2 - - + -
118C PHE* 3.3 57.0 + - + +
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Residues in contact with GLU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B VAL* 3.6 4.9 - - - +
57B LYS* 2.8 57.3 + - - +
59B SER* 5.3 2.3 + - - -
63B SER 4.7 2.2 - - - +
64B LEU* 1.3 76.8 - - - +
66B TRP* 1.3 66.1 + - - +
67B ILE* 3.2 3.6 + - - +
80B ASN* 5.6 2.5 - - - +
82B LYS* 2.4 40.1 + - + +
83B PHE* 3.7 30.5 - - + -
118C PHE* 4.5 0.4 - - - -
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Residues in contact with TRP 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ASN* 3.0 23.2 + - + -
55B TRP 4.1 8.7 - - - -
56B VAL* 4.5 5.8 - - + -
65B GLU* 1.3 69.8 - - - +
67B ILE* 1.3 65.3 + - - +
68B GLY* 3.6 17.4 + - - -
69B ASN* 3.2 29.2 - - - -
78B SER* 3.6 17.3 - - - -
79B TYR 4.3 12.6 - - - -
80B ASN* 3.3 27.6 + - + +
83B PHE* 3.9 3.1 - - - -
123B TYR* 4.4 3.6 - + - -
125B PHE* 3.5 26.5 - + - -
114C ILE* 4.5 8.5 - - + -
115C PRO* 3.6 36.6 - - + -
116C ARG* 3.3 43.0 + - + +
118C PHE* 4.0 13.4 - - + -
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Residues in contact with ILE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B TRP* 2.9 24.7 + - + +
57B LYS* 3.7 26.2 - - + +
65B GLU 3.8 9.9 - - - +
66B TRP* 1.3 72.0 - - - +
68B GLY* 1.3 58.0 + - - +
79B TYR* 3.7 5.1 - - + -
80B ASN* 2.9 31.6 + - - +
83B PHE* 3.9 31.1 - - + +
87B ALA* 3.8 26.7 - - + -
89B LEU* 5.4 3.8 - - + -
100B MET* 3.7 27.1 - - - -
102B LEU* 5.6 1.6 - - + -
113B TYR* 3.9 13.0 - - + -
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Residues in contact with GLY 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ASN* 3.3 2.8 - - - +
55B TRP 2.9 26.3 + - - -
66B TRP* 3.6 16.1 + - - -
67B ILE* 1.3 84.3 - - - +
69B ASN* 1.3 59.9 + - - -
78B SER 3.2 13.0 - - - -
79B TYR* 4.2 3.1 - - - -
89B LEU* 3.7 14.4 - - - +
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Residues in contact with ASN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B TYR* 3.7 29.5 - - + -
53B MET 3.1 10.5 - - - +
54B ASN* 3.2 11.0 - - - +
66B TRP* 3.2 21.5 - - + -
68B GLY* 1.3 72.8 - - - -
70B ILE* 1.3 67.1 + - - +
76B GLY 4.2 3.0 + - - -
77B THR* 3.5 1.6 - - - -
78B SER* 2.9 53.1 + - - -
89B LEU* 3.5 8.7 - - - +
123B TYR* 3.1 26.6 + - - +
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Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B TYR* 3.5 6.5 - - - -
53B MET* 2.9 55.6 + - + +
55B TRP* 5.5 2.2 - - - +
69B ASN* 1.3 76.8 - - - +
71B ASN* 1.3 65.4 + - - +
72B PRO* 3.3 5.5 - - - +
75B GLY* 3.9 19.7 - - - -
76B GLY 3.1 5.4 - - - -
77B THR* 3.9 11.2 - - + -
89B LEU* 3.9 21.3 - - + +
90B THR* 3.6 39.7 - - - +
91B VAL* 3.7 19.1 - - + -
98B ALA* 5.2 2.2 - - + -
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Residues in contact with ASN 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B TYR* 3.4 31.0 + - + -
70B ILE* 1.3 70.9 - - - +
72B PRO* 1.3 60.4 - - - +
73B ASN* 3.2 30.9 + - - +
74B ASN* 3.5 13.7 + - - +
75B GLY* 2.4 41.9 + - - -
76B GLY* 2.6 25.4 + - - +
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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