Contacts of the strand formed by residues 67 - 75 (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 LYS 67 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19X THR* 4.4 21.4 + - - +
20X GLY* 3.3 13.2 - - - +
21X VAL* 4.4 9.3 - - + +
37X ASP* 4.7 7.4 + - - -
65X GLY 3.5 3.4 + - - -
66X ASP* 1.3 73.5 - - - +
68X VAL* 1.3 63.9 + - - +
86X VAL* 3.3 9.0 - - - +
87X SER* 3.0 33.1 + - - +
88X GLN* 2.8 43.6 + - - +
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Residues in contact with VAL 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19X THR* 3.2 8.5 - - - -
20X GLY 2.8 45.3 + - - +
22X VAL* 3.6 33.4 - - + -
34X ILE* 4.4 5.4 - - + -
62X ILE* 3.9 22.0 - - + -
66X ASP* 4.1 6.1 - - + +
67X LYS* 1.3 79.8 - - - +
69X ALA* 1.3 59.8 + - - +
70X PHE* 4.0 13.2 - - + -
84X ILE* 4.0 20.4 - - + -
85X LYS 3.2 14.6 - - - +
87X SER* 3.6 6.0 - - - -
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Residues in contact with ALA 69 (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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18X ALA 3.4 8.5 - - - +
19X THR* 4.3 6.7 - - + -
68X VAL* 1.3 72.7 - - - +
70X PHE* 1.3 63.2 + - - +
83X ASP* 4.8 1.4 - - - +
84X ILE* 3.5 1.2 - - - +
85X LYS* 2.9 49.3 + - + +
86X VAL 5.4 0.2 - - - +
87X SER* 3.4 19.1 - - - +
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Residues in contact with PHE 70 (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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16X ILE 3.9 0.3 - - - +
17X SER* 3.4 3.3 - - - -
18X ALA* 2.9 53.3 + - + +
19X THR 3.8 23.8 - - - -
34X ILE* 3.8 24.0 - - + -
36X HIS* 4.2 6.1 - - + -
51X PHE* 3.6 43.3 - + - -
68X VAL* 4.0 13.9 - - + -
69X ALA* 1.3 78.3 - - - +
71X ASN* 1.3 63.6 + - - +
72X PHE* 3.8 13.0 - + - -
81X LEU* 3.7 18.8 - - + -
83X ASP* 3.4 16.6 - - - +
84X ILE* 3.9 13.7 - - + -
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Residues in contact with ASN 71 (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* 3.6 21.0 - - + +
16X ILE 3.2 4.2 - - - +
17X SER* 2.5 36.2 + - - -
70X PHE* 1.3 75.9 - - - +
72X PHE* 1.3 63.4 + - - +
81X LEU* 3.5 5.2 - - - +
82X GLN* 2.8 26.6 + - + -
83X ASP* 2.9 43.3 + - - +
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Residues in contact with PHE 72 (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* 3.6 2.3 - - - -
16X ILE* 2.8 69.9 + - + +
18X ALA* 4.3 2.5 - - + -
39X ILE* 3.9 16.8 - - + -
42X VAL* 4.9 2.7 - - + -
44X TRP* 4.0 18.4 - + - -
51X PHE* 3.7 28.3 - + + -
70X PHE* 3.8 15.3 - + - -
71X ASN* 1.3 76.2 - - - +
73X VAL* 1.3 70.9 + - - +
74X GLN* 4.1 19.5 - - + -
79X SER* 3.8 20.0 - - - -
80X LEU 3.1 20.6 - - - +
81X LEU* 4.1 8.3 - - + -
82X GLN* 4.1 2.2 - - - +
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Residues in contact with VAL 73 (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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13X PRO* 3.7 19.5 - - + +
14X GLN 3.6 18.4 - - - +
15X VAL* 3.9 16.4 - - + -
16X ILE* 5.3 0.4 - - - -
72X PHE* 1.3 77.8 - - - +
74X GLN* 1.3 63.0 + - - +
75X GLN* 3.7 27.7 + - + +
78X LEU 3.5 1.2 - - - +
79X SER* 3.4 4.0 - - - -
80X LEU* 2.8 41.8 + - + +
82X GLN* 3.7 30.5 - - - +
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Residues in contact with GLN 74 (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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13X PRO* 3.8 14.0 - - - +
14X GLN* 4.6 6.8 + - - +
16X ILE* 5.2 4.1 - - + +
42X VAL* 3.4 26.9 - - + +
44X TRP* 3.6 28.2 - - - +
72X PHE* 4.1 16.8 - - + -
73X VAL* 1.3 73.2 - - - +
75X GLN* 1.3 63.5 + - - +
78X LEU 3.6 6.1 - - - +
79X SER* 4.7 5.8 + - - +
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Residues in contact with GLN 75 (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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13X PRO* 3.8 23.7 - - + +
73X VAL* 3.7 24.4 + - + +
74X GLN* 1.3 75.8 - - - +
76X GLY* 1.3 68.6 + - - +
77X ASN* 3.3 2.6 - - - +
78X LEU* 3.2 22.7 + - - +
80X LEU* 3.9 22.4 - - + +
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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