Contacts of the strand formed by residues 78 - 86 (chain X) in PDB entry 1ZEQ
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 LEU 78 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X LYS* 3.9 12.6 - - - +
52X THR* 3.9 20.4 - - + +
73X VAL 3.5 1.6 - - - +
74X GLN* 3.6 4.7 - - - +
75X GLN 3.2 27.6 + - - +
76X GLY 3.7 11.0 - - - +
77X ASN* 1.3 86.2 - - + +
79X SER* 1.3 63.9 + - - +
80X LEU* 3.8 25.4 - - + -
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Residues in contact with SER 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44X TRP* 4.0 20.1 - - - -
49X MET* 5.1 3.3 - - - +
50X ARG 4.4 9.7 + - - -
51X PHE* 3.6 26.8 - - - +
52X THR* 2.8 29.2 + - - -
72X PHE* 3.8 13.6 - - - -
73X VAL 3.4 6.1 - - - -
74X GLN* 4.7 6.0 + - - +
78X LEU* 1.3 74.1 + - - +
80X LEU* 1.3 62.7 + - - +
81X LEU 3.6 0.5 + - - -
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Residues in contact with LEU 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52X THR* 3.7 22.7 - - + -
54X THR* 4.0 20.9 - - + -
72X PHE* 3.1 2.7 - - - -
73X VAL* 2.8 44.5 + - + +
75X GLN* 3.9 42.0 - - + +
78X LEU* 3.8 26.9 - - + -
79X SER* 1.3 71.2 - - - +
81X LEU* 1.3 63.8 + - - +
82X GLN* 3.1 7.9 - - - +
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Residues in contact with LEU 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32X ILE* 3.7 34.5 - - + -
34X ILE* 4.9 2.0 - - + -
51X PHE* 3.8 27.6 - - + -
52X THR 2.8 26.4 + - - +
53X ILE* 4.3 3.8 - - + -
54X THR* 4.5 5.0 + - - +
57X THR* 2.7 39.8 + - + -
70X PHE* 3.7 35.9 - - + -
71X ASN 3.5 8.3 - - - +
72X PHE* 4.4 3.1 - - + -
79X SER 3.6 0.6 + - - -
80X LEU* 1.3 71.4 - - - +
82X GLN* 1.3 62.9 + - - +
83X ASP 4.4 3.8 - - - +
84X ILE* 4.9 6.3 - - + -
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Residues in contact with GLN 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15X VAL* 4.3 14.6 - - + +
54X THR* 5.9 0.3 - - - +
56X GLN 4.2 1.8 - - - +
57X THR* 3.7 2.4 - - - +
58X LYS* 2.9 27.3 + - - +
71X ASN* 2.8 18.3 + - + +
72X PHE* 4.2 3.4 - - - -
73X VAL* 3.7 32.7 - - + +
80X LEU* 3.1 22.7 - - - +
81X LEU* 1.3 78.2 - - - +
83X ASP* 1.3 72.9 + - - +
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Residues in contact with ASP 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57X THR* 4.3 3.4 - - - -
58X LYS* 3.4 28.9 - - + +
69X ALA 4.8 1.4 - - - +
70X PHE* 3.4 6.1 - - - +
71X ASN* 2.9 56.3 + - - +
81X LEU* 3.6 2.9 - - - +
82X GLN* 1.3 85.5 - - - +
84X ILE* 1.3 66.8 + - - +
85X LYS* 5.9 3.8 - - - +
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Residues in contact with ILE 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22X VAL* 4.8 0.2 - - + -
32X ILE* 4.3 11.2 - - + -
34X ILE* 3.9 28.0 - - + -
57X THR* 4.7 3.4 - - + -
58X LYS 3.2 11.7 + - - +
59X MET* 3.8 31.0 - - - -
60X SER* 2.8 18.1 + - - +
62X ILE* 4.0 27.8 - - + -
68X VAL* 4.0 21.8 - - + -
69X ALA 3.5 7.4 - - - +
70X PHE* 3.9 11.4 - - + -
81X LEU* 4.9 5.8 - - + -
83X ASP* 1.3 79.9 - - - +
85X LYS* 1.3 66.9 + - - +
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Residues in contact with LYS 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X SER* 3.3 15.0 - - - +
62X ILE* 4.4 2.2 - - - -
68X VAL* 3.2 9.4 - - - -
69X ALA* 2.9 48.4 + - + +
83X ASP* 5.9 3.8 - - - +
84X ILE* 1.3 78.4 - - - +
86X VAL* 1.3 72.2 + - + +
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Residues in contact with VAL 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X SER* 4.5 0.8 + - - -
61X GLU 4.0 15.2 + - - +
62X ILE* 4.4 4.1 - - + +
63X LYS* 5.7 0.9 - - - +
66X ASP* 3.5 35.9 - - + +
67X LYS 3.3 7.0 - - - +
68X VAL* 4.2 0.7 - - - +
85X LYS* 1.3 87.7 - - + +
87X SER* 1.3 59.5 + - - +
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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