Contacts of the strand formed by residues 72 - 78 (chain B) in PDB entry 5LEZ
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 MET 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B LYS 3.9 0.3 - - - -
68B LEU* 2.9 32.4 + - + -
69B ASN* 3.0 24.7 + - - +
70B GLU 3.6 1.6 - - - -
71B ASP* 1.3 86.9 - - + +
73B ALA* 1.3 64.2 + - - +
105B ILE 4.4 9.6 - - - +
107B CYS* 3.7 54.7 - - + +
110B LEU* 3.7 29.6 - - + -
111B VAL* 5.0 0.2 - - + -
136B TYR* 4.5 21.1 - - + -
137B ILE 3.3 13.5 - - - +
216B LEU* 4.2 1.3 - - - -
225B ILE* 3.8 8.5 - - - +
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Residues in contact with ALA 73 (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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45B LEU* 4.7 4.0 - - + -
65B ILE* 4.7 7.4 - - + -
66B TYR 3.1 17.7 - - - +
67B LYS* 4.3 2.9 - - - -
68B LEU* 4.2 5.9 - - - +
72B MET* 1.3 75.9 - - - +
74B CYS* 1.3 65.3 + - - +
136B TYR* 3.5 2.4 - - - +
137B ILE* 2.8 48.1 + - + +
214B ALA* 6.1 0.7 - - + -
216B LEU* 4.4 0.6 - - + +
225B ILE* 4.4 20.9 - - + -
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Residues in contact with CYS 74 (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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45B LEU* 3.7 7.9 - - - +
64B LYS 3.7 0.3 - - - +
65B ILE* 3.4 4.0 - - - -
66B TYR* 2.8 41.2 + - - -
68B LEU* 3.8 25.8 - - + -
73B ALA* 1.3 77.5 - - - +
75B SER* 1.3 62.2 + - - +
76B VAL* 4.5 0.9 - - - -
87B THR* 3.7 30.1 - - - -
90B LEU* 4.4 0.7 - - - -
134B LEU* 4.1 15.0 - - + -
135B LEU 3.0 14.1 - - - +
136B TYR* 4.2 9.9 - - + -
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Residues in contact with SER 75 (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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34B CYS* 3.2 27.5 - - - -
45B LEU* 3.9 12.9 - - - +
47B ALA* 4.1 2.8 - - - +
64B LYS* 3.0 23.5 + - - +
65B ILE* 3.7 18.6 - - - +
74B CYS* 1.3 74.3 - - - +
76B VAL* 1.3 71.1 + - - +
134B LEU* 3.3 6.1 - - - +
135B LEU* 2.8 31.2 + - - +
164B ILE* 4.8 0.2 - - - +
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Residues in contact with VAL 76 (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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34B CYS* 4.2 4.3 - - - -
64B LYS* 3.0 40.5 + - + +
66B TYR* 3.9 27.4 - - + +
74B CYS* 4.5 0.7 - - - -
75B SER* 1.3 85.3 + - - +
77B ALA* 1.3 63.8 + - - +
78B GLY 5.7 0.2 - - - +
80B THR* 5.9 3.1 - - + -
83B ALA* 3.8 32.3 - - + -
87B THR* 4.4 5.4 - - + -
132B VAL* 4.1 2.5 - - + -
133B SER 3.5 6.5 - - - +
134B LEU* 3.7 25.8 - - + -
164B ILE* 4.6 2.7 - - - -
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Residues in contact with ALA 77 (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 ILE* 3.3 18.3 - - + +
31B ALA* 4.0 7.2 - - + -
32B GLY 4.0 18.4 - - - +
34B CYS* 4.6 1.1 - - + -
64B LYS* 4.6 2.2 - - - +
76B VAL* 1.3 78.4 - - - +
78B GLY* 1.3 57.9 + - - +
132B VAL* 3.6 3.2 - - - -
133B SER 2.9 31.6 + - - -
164B ILE* 3.7 24.7 - - + -
165B GLY* 4.3 4.3 - - - -
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Residues in contact with GLY 78 (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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27B ALA* 4.9 2.7 - - - -
28B ILE* 3.9 11.7 - - - -
31B ALA* 3.3 22.4 - - - +
76B VAL* 4.4 0.6 - - - +
77B ALA* 1.3 74.1 - - - +
79B ILE* 1.3 69.6 + - - -
80B THR* 3.3 7.1 + - - -
83B ALA* 6.1 0.2 - - - -
131B GLY 3.2 8.5 - - - -
132B VAL* 4.6 0.9 - - - -
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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