Contacts of the strand formed by residues 70 - 75 (chain D) in PDB entry 4NQC
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 TYR 70 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D GLN* 3.2 7.6 + - - -
21D ASN* 2.7 38.1 + - + -
22D CYS 3.4 9.2 - - - -
23D THR* 3.9 16.4 - - + -
24D TYR* 3.6 2.7 - - - -
63D PHE* 3.9 24.9 - + - -
64D LEU* 3.6 4.9 - - - +
65D SER* 2.9 35.4 + - - +
68D LYS* 3.8 24.9 - - + +
69D GLY* 1.3 76.7 - - - +
71D SER* 1.3 76.8 + - - +
72D TYR* 3.2 22.9 - + - -
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Residues in contact with SER 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D CYS* 2.8 32.7 + - - +
32D LEU* 3.5 34.4 - - - +
34D TRP* 3.1 21.8 + - - -
49D ASN* 5.2 2.8 + - - -
63D PHE 2.7 22.8 + - - -
64D LEU* 4.3 4.4 - - - +
70D TYR* 1.3 88.2 - - - +
72D TYR* 1.3 60.7 + - - +
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Residues in contact with TYR 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D GLN* 3.6 37.0 - - + -
20D ILE 3.1 12.3 - - - +
21D ASN* 3.6 7.6 - - - +
34D TRP* 4.0 3.0 + - - -
54D LEU* 3.9 23.0 - - + +
61D SER 4.9 0.2 - - - -
62D SER* 3.4 4.0 - - - -
63D PHE* 3.0 74.5 + + + +
70D TYR* 3.2 19.7 - + - +
71D SER* 1.3 79.8 + - - +
73D LEU* 1.3 58.5 + - - +
74D LEU* 3.8 29.8 - - + +
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Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D VAL 3.7 1.6 - - - +
19D GLN* 3.5 1.4 - - - -
20D ILE* 2.8 39.8 + - + +
34D TRP* 3.7 40.3 - - + -
46D LEU* 3.9 12.3 - - + -
47D SER* 4.6 1.3 - - - +
60D PHE* 4.3 19.7 - - + -
61D SER 3.5 8.3 - - - +
62D SER* 3.6 21.1 - - - +
72D TYR* 1.3 73.8 - - - +
74D LEU* 1.3 58.8 + - - +
75D LEU* 3.7 20.0 - - + +
86D TYR* 3.5 34.5 - - + -
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Residues in contact with LEU 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ILE* 3.7 22.9 - - + -
18D VAL 3.5 13.9 - - - +
19D GLN* 3.8 24.5 - - + +
54D LEU* 5.6 3.8 - - + -
59D ARG 3.6 1.6 - - - +
60D PHE* 3.4 6.4 - - - +
61D SER* 2.8 47.2 + - - +
72D TYR* 3.8 21.9 - - + +
73D LEU* 1.3 73.0 - - - +
75D LEU* 1.3 60.6 + - - +
76D LYS* 3.7 31.9 - - + +
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Residues in contact with LEU 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ILE* 3.3 6.6 - - - +
18D VAL* 3.0 40.6 + - + +
20D ILE* 4.4 8.3 - - + -
59D ARG* 3.6 4.7 - - - +
60D PHE* 3.7 26.5 - - + -
73D LEU* 3.7 40.6 - - + +
74D LEU* 1.3 71.0 - - - +
76D LYS* 1.3 62.5 + - - +
78D LEU* 3.8 14.3 - - + +
82D ASP* 4.1 13.2 - - + +
86D TYR* 3.7 23.8 - - + +
105D LEU* 3.8 17.7 - - + -
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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