Contacts of the strand formed by residues 63 - 71 (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 VAL 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B THR* 2.9 21.5 + - - -
34B TYR* 3.7 35.7 - - + -
62B LYS* 1.3 71.5 - - - +
64B MET* 1.3 61.1 + - - +
65B TYR* 3.7 18.4 - - + +
84B ASN* 4.8 1.3 - - - +
85B TRP 3.4 10.5 - - - +
86B VAL* 4.3 18.4 - - + -
90B VAL* 3.8 30.9 - - + +
94B ARG* 5.0 2.2 - - + +
95B LYS* 5.1 0.9 - - - -
98B CYS* 3.9 24.0 - - + -
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Residues in contact with MET 64 (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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31B LEU* 3.9 29.8 - - + -
32B TYR 3.3 10.3 - - - +
33B THR* 3.7 25.4 - - + +
44B ALA* 4.2 7.4 - - + -
57B HIS 3.9 7.2 - - - +
58B PHE* 4.0 7.9 - - + -
59B GLU* 3.6 52.3 - - - +
62B LYS* 3.8 13.2 - - + +
63B VAL* 1.3 80.5 - - - +
65B TYR* 1.3 72.5 + - - +
85B TRP* 2.9 46.3 + - + +
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Residues in contact with TYR 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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31B LEU* 3.5 3.2 - - - -
32B TYR* 2.9 45.4 + - + +
33B THR 5.2 0.2 - - - -
34B TYR* 2.5 44.7 + + - -
41B LEU* 4.0 21.3 - - + -
63B VAL* 3.7 13.2 - - + +
64B MET* 1.3 79.5 - - - +
66B GLY* 1.3 60.0 + - - +
67B PHE* 4.6 3.6 - - + -
82B LEU* 3.8 17.9 - - + -
83B ILE 3.3 3.6 - - - -
84B ASN* 3.4 30.0 + - + -
98B CYS 3.5 16.3 + - - -
101B HIS* 4.0 2.6 - - + +
102B VAL* 4.0 15.4 - - + +
105B VAL* 3.9 29.8 - - + -
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Residues in contact with GLY 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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30B ALA 3.6 5.4 - - - -
31B LEU* 3.8 13.1 - - - +
54B LEU* 4.3 17.2 - - - +
58B PHE* 4.5 1.9 - - - -
64B MET 4.2 0.4 - - - -
65B TYR* 1.3 71.5 - - - +
67B PHE* 1.3 63.9 + - - -
68B CYS 4.0 0.2 + - - -
81B VAL 3.5 1.6 - - - +
82B LEU* 3.3 4.2 - - - +
83B ILE* 2.8 44.2 + - - +
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Residues in contact with PHE 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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17B TYR* 3.2 38.6 - + + -
20B VAL* 4.9 2.4 - - + +
29B TRP* 3.0 8.5 - - - +
30B ALA* 2.8 39.3 + - + +
32B TYR* 3.8 20.0 - + + -
54B LEU* 4.8 0.2 - - - -
65B TYR* 4.5 1.3 - - + -
66B GLY* 1.3 71.9 - - - -
68B CYS* 1.3 60.7 + - - +
80B TYR* 5.7 1.3 - + + -
81B VAL 3.4 8.1 - - - -
82B LEU* 3.3 29.6 - - + -
105B VAL* 4.2 12.3 - - + -
109B PHE* 3.2 43.3 - + + -
112B VAL* 3.2 33.7 - - + -
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Residues in contact with CYS 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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20B VAL* 4.8 0.4 - - - -
28B ASP 3.3 8.5 - - - -
29B TRP* 4.3 1.8 - - + -
50B GLY* 3.9 8.7 - - - -
51B LEU* 3.7 48.9 - - + -
54B LEU* 4.1 9.0 - - + -
66B GLY 5.2 0.2 - - - +
67B PHE* 1.3 75.4 - - - +
69B SER* 1.3 75.1 + - - +
70B VAL* 3.8 9.6 + - + +
80B TYR* 3.7 6.4 - - - -
81B VAL* 2.9 39.1 + - + +
83B ILE* 5.5 0.4 - - + -
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Residues in contact with SER 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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20B VAL* 3.8 20.4 + - - +
28B ASP* 2.8 31.1 + - - +
50B GLY* 5.2 0.3 - - - -
68B CYS* 1.3 79.5 - - - +
70B VAL* 1.3 63.7 + - - +
78B PRO* 3.5 22.3 - - - +
79B LYS 3.7 4.5 - - - -
80B TYR* 3.5 23.4 + - - -
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Residues in contact with VAL 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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50B GLY* 6.3 0.2 - - - -
51B LEU* 4.3 20.6 - - + +
68B CYS* 3.9 20.6 - - - +
69B SER* 1.3 80.2 + - - +
71B LYS* 1.3 71.6 + - - +
72B ASP* 4.1 0.8 + - - -
78B PRO* 3.5 3.5 - - - +
79B LYS* 2.8 42.5 + - + +
81B VAL* 4.5 13.2 - - + -
129B ILE* 5.4 1.6 - - + -
130B GLY* 5.6 5.8 - - - -
133B LEU* 4.6 16.2 - - + -
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Residues in contact with LYS 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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70B VAL* 1.3 82.7 - - - +
72B ASP* 1.3 61.1 + - - +
73B SER 3.4 16.5 + - - +
74B GLN 5.1 3.8 - - - +
76B ALA 4.5 13.2 - - - +
77B LEU 4.9 0.2 - - - -
78B PRO* 4.4 11.4 - - + -
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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