Contacts of the strand formed by residues 62 - 68 (chain B) in PDB entry 4Z18
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 LYS 62 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLU* 3.4 7.5 - - - +
59B MET* 2.8 44.4 + - + +
60B GLU* 3.5 15.3 + - - -
61B ASP* 1.3 90.6 - - - +
63B ASN* 1.3 62.5 + - - +
64B ILE* 4.1 0.3 - - - +
78B HIS* 4.0 38.8 - - + +
80B SER* 4.2 10.9 + - - -
81B TYR* 3.7 30.9 + - + +
107B GLN* 4.4 19.8 + - - +
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Residues in contact with ASN 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 3.5 26.4 - - + +
61B ASP 5.0 4.0 + - - -
62B LYS* 1.3 75.4 - - - +
64B ILE* 1.3 61.2 + - - +
65B ILE 5.3 0.2 - - - +
66B GLN* 3.6 20.3 + - + +
76B VAL* 3.2 48.4 + - + +
77B GLN* 4.2 1.1 - - - -
78B HIS* 3.0 32.8 + - - +
81B TYR* 3.9 2.4 - - - -
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B TRP 2.9 13.5 + - - +
58B GLU* 3.5 30.7 - - - +
59B MET* 3.7 6.5 - - + +
62B LYS 4.1 2.5 - - - +
63B ASN* 1.3 77.9 - - - +
65B ILE* 1.3 63.9 + - + +
66B GLN 4.3 0.2 - - - -
74B LEU* 4.9 1.0 - - - +
77B GLN* 3.1 35.7 + - - +
81B TYR* 3.9 27.6 - - + +
85B ALA* 3.8 26.0 - - + -
99B LEU* 3.9 21.1 - - + -
101B ILE* 4.4 1.8 - - + -
112B TYR* 3.6 31.9 - - + -
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Residues in contact with ILE 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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55B VAL 4.2 4.9 - - - +
56B TYR* 3.2 5.2 - - - +
57B TRP* 2.8 45.5 + - + +
58B GLU* 5.4 0.3 - - - +
63B ASN* 6.1 0.2 - - - -
64B ILE* 1.3 87.7 - - + +
66B GLN* 1.3 76.4 + - - +
67B PHE* 4.2 3.8 - - + +
72B GLU* 3.6 23.3 - - - +
73B ASP 5.2 1.1 - - - -
74B LEU* 4.8 2.5 - - + -
77B GLN* 4.8 2.2 - - - +
85B ALA* 3.9 9.6 - - + +
86B ARG* 3.8 24.9 - - - +
87B LEU* 4.1 23.1 - - + +
99B LEU* 3.7 25.6 - - + -
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Residues in contact with GLN 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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55B VAL 3.7 2.9 - - - -
56B TYR* 3.1 49.7 + - + -
58B GLU* 6.2 0.4 - - + -
63B ASN* 3.6 24.0 + - + +
65B ILE* 1.3 79.9 - - - +
67B PHE* 1.3 57.3 + - - +
68B VAL* 3.9 3.5 - - + +
72B GLU* 3.3 4.5 - - - +
73B ASP* 2.6 64.6 + - + +
74B LEU* 5.4 0.2 - - - +
76B VAL* 3.6 24.9 - - + +
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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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50B LEU* 3.9 27.1 - - + -
53B LEU* 4.0 27.8 - - + -
54B ILE* 3.2 8.1 - - - -
55B VAL* 2.7 40.8 + - + +
65B ILE* 4.6 1.8 - - + -
66B GLN* 1.3 71.4 - - - +
68B VAL* 1.3 63.2 + - - +
70B GLY* 3.3 41.1 - - - -
71B GLU 3.6 4.7 - - - -
72B GLU* 3.9 24.0 - - + -
87B LEU* 3.9 25.6 - - + -
89B LYS* 4.5 16.6 - - + -
92B LEU* 4.1 12.3 - - + -
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Residues in contact with VAL 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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53B LEU 4.2 3.4 - - - -
54B ILE* 4.1 22.7 - - + -
56B TYR* 3.4 35.0 - - + +
66B GLN* 3.9 8.6 + - + +
67B PHE* 1.3 80.4 - - - +
69B HIS* 1.3 102.6 + - + +
70B GLY 3.1 2.9 - - - -
71B GLU* 2.9 20.5 + - - +
73B ASP* 5.2 7.1 - - + +
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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