Contacts of the strand formed by residues 67 - 73 (chain L) in PDB entry 2ZHX
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 67 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7L ILE* 3.6 33.4 - - + -
57L LEU* 5.3 0.9 - - + -
58L LEU 4.0 5.2 - - - +
59L THR* 4.3 7.0 - - + -
65L TYR 3.3 9.6 - - - +
66L LYS* 1.3 89.2 - - + +
68L TRP* 1.3 60.1 + - - +
84L LEU* 4.0 25.8 - - + +
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Residues in contact with TRP 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L VAL* 3.5 29.6 - - + -
33L ILE* 3.8 21.3 - - + -
35L ASN* 3.1 43.1 - - + -
36L LYS 4.5 0.4 - - - -
37L PRO* 3.5 27.3 - - + +
38L GLU 5.0 1.9 - - - +
41L ILE* 3.3 22.2 - - + -
58L LEU* 2.9 24.0 + - + +
59L THR* 4.4 2.5 - - - -
60L SER 5.1 0.4 - - - +
66L LYS 4.3 4.3 - - - +
67L PRO* 1.3 76.6 - - - +
69L ALA* 1.3 76.9 + - + +
83L MET* 3.8 18.4 - - + +
84L LEU* 2.9 29.8 + - - +
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Residues in contact with ALA 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L ILE* 4.4 11.2 - - + -
57L LEU* 3.7 4.3 - - - +
58L LEU* 2.8 37.4 + - + +
68L TRP* 1.3 105.7 - - + +
70L LEU* 1.3 59.9 + - - +
81L ILE* 5.0 1.6 - - + -
82L LYS 3.7 11.9 - - - +
83L MET* 4.1 13.9 - - - -
84L LEU* 4.0 6.5 - - - -
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Residues in contact with LEU 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L ILE* 5.1 9.2 - - + +
11L GLU* 3.4 37.9 - - + +
12L THR* 3.9 14.4 - - + -
55L VAL* 4.5 9.9 - - + -
56L MET 3.4 9.2 - - - +
57L LEU* 4.3 13.0 - - + -
69L ALA* 1.3 75.0 - - - +
71L VAL* 1.3 85.7 + - - +
72L ILE* 3.6 33.4 - - + -
80L LYS 4.1 1.0 - - - +
81L ILE* 3.8 1.0 - - - +
82L LYS* 3.0 36.7 + - + +
84L LEU* 3.5 14.6 - - + +
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Residues in contact with VAL 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195K LEU* 4.5 6.1 - - + -
33L ILE* 3.8 31.0 - - + -
54L ASN 3.7 1.2 - - - +
55L VAL* 3.7 0.3 - - - -
56L MET* 2.7 69.1 + - + +
58L LEU* 3.9 6.3 - - + -
70L LEU* 1.3 82.1 - - - +
72L ILE* 1.3 69.4 + - - +
79L ASN* 3.9 31.2 - - + +
80L LYS 4.0 2.9 - - - -
81L ILE* 3.8 15.7 - - + -
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Residues in contact with ILE 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L THR* 3.9 19.3 - - + -
53L GLU* 3.7 40.2 - - + +
54L ASN 3.9 2.7 - - - +
55L VAL* 4.6 15.9 - - + -
70L LEU* 3.6 21.8 - - + -
71L VAL* 1.3 80.2 - - - +
73L GLN* 1.3 61.7 + - - +
79L ASN* 3.4 1.7 - - - -
80L LYS* 2.9 59.2 + - + +
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Residues in contact with GLN 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96K ASN* 5.5 0.3 + - - -
194K PRO* 3.1 35.5 + - - +
195K LEU* 4.4 1.6 - - - +
198K SER* 5.8 1.4 + - - -
53L GLU* 3.1 9.6 - - - +
54L ASN* 2.9 64.8 + - + +
56L MET* 3.7 11.6 - - + +
71L VAL 4.1 0.8 - - - -
72L ILE* 1.3 72.7 - - - +
74L ASP* 1.3 71.1 + - - +
77L GLY* 3.6 19.1 + - - +
78L GLU 3.5 4.5 - - - -
79L ASN* 3.3 25.3 + - - +
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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