Contacts of the strand formed by residues 57 - 63 (chain B) in PDB entry 5V1Y
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 ILE 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 4.1 8.3 - - + -
49B ILE* 3.7 22.0 - - + -
50B GLN 3.7 0.9 - - - -
51B GLN* 3.9 35.4 - - + +
55B SER 4.2 2.0 - - - +
56B LEU* 1.3 74.7 - - - +
58B HIS* 1.3 63.6 + - - +
73B LEU 3.6 0.2 - - - +
74B ILE* 3.4 5.4 - - - +
75B ILE 2.9 42.0 + - - +
127B TYR 3.8 9.9 - - - +
128B LEU* 3.7 23.3 - - + -
131B PRO* 3.6 23.3 - - + -
132B PRO* 3.9 17.7 - - + -
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Residues in contact with HIS 58 (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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48B TYR 3.7 1.0 - - - +
49B ILE* 3.2 6.9 - - - +
50B GLN* 2.8 39.5 + - + +
52B THR* 2.9 43.5 + - + +
54B ASP* 5.1 1.6 + - - -
56B LEU* 3.6 12.0 - - + +
57B ILE* 1.3 83.4 - - - +
59B PHE* 1.3 59.4 + - - +
60B CYS* 3.9 9.8 - - - -
72B ASP* 2.7 34.0 + - - +
73B LEU 3.2 4.3 - - - -
74B ILE* 3.6 29.3 - - + +
42D ARG* 5.6 2.0 + - - -
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Residues in contact with PHE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 3.8 27.4 - - + -
48B TYR 3.8 2.5 - - - -
49B ILE* 4.3 14.8 - - + -
57B ILE* 4.2 0.8 - - - +
58B HIS* 1.3 71.1 - - - +
60B CYS* 1.3 66.2 + - - +
61B TRP* 5.5 0.4 - - + -
71B ASP* 4.0 3.3 - - + +
72B ASP* 3.6 1.0 + - - -
73B LEU* 2.8 43.4 + - + +
75B ILE* 4.0 21.9 - - + +
82B PHE* 4.4 10.1 - + - -
96B LEU* 3.9 27.4 - - + -
105B LEU* 5.6 0.2 - - + -
107B PHE* 3.6 38.4 - + - -
124B VAL* 4.1 18.4 - - + -
128B LEU* 4.4 15.3 - - + -
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Residues in contact with CYS 60 (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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46B LEU 4.3 0.4 - - - -
47B VAL* 3.3 9.2 - - - +
48B TYR* 2.8 74.5 + - + +
50B GLN* 5.4 0.7 - - - -
58B HIS* 3.9 15.9 - - - -
59B PHE* 1.3 82.6 - - - +
61B TRP* 1.3 61.6 + - - +
62B LYS 4.3 0.2 - - - -
69B VAL* 4.4 2.5 - - + -
71B ASP* 3.1 8.5 - - - +
72B ASP* 3.7 31.4 - - - -
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Residues in contact with TRP 61 (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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28B ALA 2.9 24.9 + - - -
29B GLY* 4.1 0.2 - - - -
30B LYS* 3.6 37.8 - - + +
41B ASP* 5.5 1.3 - - - -
43B ARG* 3.7 49.4 - - + -
44B LYS 4.3 0.7 - - - -
45B GLY* 3.6 23.1 - - - -
46B LEU 3.3 12.6 - - - -
47B VAL* 3.9 8.7 - - + -
59B PHE* 5.5 0.2 - - + -
60B CYS* 1.3 73.5 - - - +
62B LYS* 1.3 57.5 - - - +
63B ASP* 3.8 22.2 - - + -
69B VAL* 3.8 3.1 - - - -
70B GLU* 3.0 38.3 + - + -
71B ASP* 2.9 29.4 + - + +
107B PHE* 3.8 27.1 - + + -
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Residues in contact with LYS 62 (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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22B TYR* 4.6 4.5 + - - +
45B GLY* 3.1 5.7 - - - -
46B LEU* 2.9 50.7 + - + +
48B TYR* 4.1 18.2 - - + -
61B TRP* 1.3 76.7 - - - +
63B ASP* 1.3 69.0 + - - +
64B ARG* 3.5 6.0 + - + +
67B GLY* 3.2 29.0 + - - +
68B ASN 3.4 16.2 - - - +
69B VAL* 4.1 13.8 - - + +
48C LYS* 5.3 7.1 - - - +
51C GLU* 6.3 1.2 - - - +
54C ARG* 4.4 18.0 - - - +
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Residues in contact with ASP 63 (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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69A VAL 4.0 8.2 - - - +
43B ARG* 3.0 40.6 + - - +
44B LYS 3.8 7.8 - - - +
61B TRP* 3.8 15.6 - - + -
62B LYS* 1.3 71.4 - - - +
64B ARG* 1.3 59.2 + - - +
65B THR* 2.8 34.2 + - - -
66B SER* 3.0 27.9 + - - +
67B GLY* 2.9 30.7 + - - -
68B ASN 2.9 11.8 + - - +
70B GLU* 5.2 1.8 - - + +
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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