Contacts of the strand formed by residues 78 - 86 (chain B) in PDB entry 5Y1Z
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 PRO 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B ILE 5.8 1.6 - - - +
69B SER* 3.5 22.0 - - - +
70B VAL 3.5 12.6 - - - +
71B LYS* 4.4 7.6 - - + -
76B ALA 3.4 5.6 - - - +
77B LEU* 1.3 92.3 - - + +
79B LYS* 1.3 60.2 + - - +
80B TYR* 3.8 29.4 - - + +
113B ASP* 4.4 1.6 - - - +
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Residues in contact with LYS 79 (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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68B CYS 3.9 0.2 - - - +
69B SER* 3.7 3.1 - - - -
70B VAL* 2.8 39.8 + - + +
72B ASP* 5.5 4.9 - - + +
77B LEU 3.7 1.9 + - - +
78B PRO* 1.3 74.1 - - - +
80B TYR* 1.3 63.4 + - - +
81B VAL* 5.4 0.4 - - - -
113B ASP* 3.2 14.1 - - - +
133B LEU* 4.0 32.3 - - + -
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Residues in contact with TYR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B TYR* 3.7 25.1 - + - +
20B VAL* 4.2 11.8 + - + -
21B ILE* 3.7 38.9 + - + +
67B PHE* 5.7 0.4 - + + -
68B CYS 3.7 3.1 - - - -
69B SER* 3.5 36.0 + - - -
78B PRO* 3.8 31.0 - - + +
79B LYS* 1.3 75.4 - - - +
81B VAL* 1.3 63.9 + - - +
111B GLY* 3.8 23.8 - - - +
112B VAL* 3.8 3.5 - - + -
113B ASP* 2.8 38.9 + - - +
114B VAL* 3.1 8.4 + - - -
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 4.9 2.7 - - + -
66B GLY 3.5 0.9 - - - +
67B PHE* 3.4 9.3 - - - -
68B CYS* 2.9 43.3 + - + +
70B VAL* 4.5 11.4 - - + -
80B TYR* 1.3 76.1 - - - +
82B LEU* 1.3 73.0 + - - +
83B ILE* 4.1 14.4 - - + -
112B VAL* 4.6 0.4 - - - -
114B VAL* 3.6 17.7 - - + +
116B VAL* 4.0 19.5 - - + -
129B ILE* 3.6 30.7 - - + -
133B LEU* 4.4 9.4 - - + -
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Residues in contact with LEU 82 (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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65B TYR* 3.8 22.2 - - + -
66B GLY 3.3 9.4 - - - +
67B PHE* 3.3 33.7 - - + -
81B VAL* 1.3 73.8 - - - +
83B ILE* 1.3 67.7 + - - +
84B ASN* 3.7 2.1 + - + +
102B VAL* 4.5 10.5 - - + -
105B VAL* 4.5 5.4 - - + -
106B ALA* 4.1 28.9 - - + +
112B VAL* 3.7 23.5 - - + +
114B VAL 3.0 7.5 + - - +
115B ILE* 3.3 18.7 - - + +
116B VAL* 2.9 25.1 + - - -
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Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 3.9 19.7 - - + -
54B LEU* 3.7 26.7 - - + -
58B PHE* 3.5 23.1 - - + -
64B MET 3.5 0.2 - - - +
65B TYR* 3.3 7.6 - - - -
66B GLY 2.8 37.9 + - - +
68B CYS* 5.5 0.2 - - + -
81B VAL* 4.1 11.9 - - + -
82B LEU* 1.3 75.6 - - - +
84B ASN* 1.3 60.9 + - - +
85B TRP* 3.3 11.3 + - + +
116B VAL* 3.4 19.3 - - + +
118B ALA* 4.1 17.7 - - + -
124B ILE* 4.0 22.4 - - + -
129B ILE* 5.1 0.9 - - + -
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Residues in contact with ASN 84 (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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63B VAL* 4.8 1.4 - - - +
64B MET 4.0 2.0 - - - -
65B TYR* 3.4 25.6 + - + -
82B LEU* 3.7 4.5 + - + +
83B ILE* 1.3 67.7 - - - +
85B TRP* 1.3 61.1 + - - +
86B VAL* 3.7 21.9 + - - +
99B ALA* 5.9 1.8 - - - +
102B VAL* 3.6 26.6 - - + +
115B ILE* 4.3 11.2 - - + -
116B VAL 2.9 8.5 + - - +
117B ASN* 3.2 30.8 + - - +
118B ALA 3.0 23.7 + - - +
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Residues in contact with TRP 85 (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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58B PHE* 3.5 57.7 - + + -
59B GLU 2.7 26.6 + - - +
60B ASN* 3.6 23.1 - - - -
62B LYS 3.3 15.6 + - - -
63B VAL* 3.4 7.8 - - - +
64B MET* 2.9 53.2 + - + +
83B ILE* 3.3 3.5 + - + -
84B ASN* 1.3 74.1 - - - +
86B VAL* 1.3 59.7 + - - +
87B GLY* 3.6 8.2 - - - +
118B ALA* 3.1 26.9 - - + -
119B SER 3.4 17.3 - - - -
120B SER* 3.4 34.1 - - - -
121B VAL* 4.0 9.2 - - + -
124B ILE* 4.7 0.9 - - + -
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Residues in contact with VAL 86 (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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62B LYS 4.4 0.9 - - - -
63B VAL* 4.3 18.2 - - + -
84B ASN* 3.9 26.2 - - - +
85B TRP* 1.3 77.8 - - - +
87B GLY* 1.3 65.4 + - - +
90B VAL* 4.6 0.2 - - + -
95B LYS* 3.4 48.6 + - + +
98B CYS* 6.2 1.1 - - + -
117B ASN* 6.4 0.7 - - + -
118B ALA 2.9 8.4 + - - +
119B SER* 2.7 34.7 + - - +
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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