Contacts of the strand formed by residues 72 - 77 (chain D) in PDB entry 1KGC
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 SER 72 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D PRO* 6.5 0.4 - - - -
22D CYS 3.1 16.2 - - - -
23D ASN* 4.6 6.5 - - - -
24D HIS* 3.3 6.8 + - - -
66D ILE* 3.8 3.3 - - - +
67D ALA* 2.9 42.1 + - - +
69D ASP* 4.1 0.7 + - - -
71D LYS* 1.3 82.2 - - - +
73D SER* 1.3 66.8 + - - +
74D THR* 5.7 0.7 + - - -
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Residues in contact with SER 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D PRO* 3.6 0.5 - - - +
22D CYS* 2.8 37.9 + - - +
24D HIS* 2.8 27.0 + - - -
32D ILE* 3.4 32.4 - - - +
34D TRP* 4.7 1.1 - - - -
64D LEU* 4.6 2.0 - - - -
65D ALA 3.2 11.9 - - - -
66D ILE* 3.8 10.5 - - - +
67D ALA 4.7 0.2 - - - +
72D SER* 1.3 75.1 + - - +
74D THR* 1.3 68.3 + - - +
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Residues in contact with THR 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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19D HIS* 3.9 20.0 - - + -
20D LEU 3.3 20.2 - - - +
21D PRO* 4.3 7.9 - - + +
34D TRP* 4.2 4.9 - - - -
64D LEU* 3.6 5.7 - - - +
65D ALA* 2.7 46.9 + - - +
72D SER* 5.7 0.5 + - - -
73D SER* 1.3 80.0 + - - +
75D LEU* 1.3 74.4 + - - +
76D ILE* 3.8 8.4 + - + -
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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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18D VAL 3.4 2.8 - - - +
20D LEU* 2.9 40.9 + - + +
34D TRP* 3.5 43.5 - - + +
46D VAL* 4.0 7.4 - - + -
47D ILE* 3.8 24.2 - - + -
62D ALA* 3.7 25.1 - - + -
63D SER 3.7 7.0 - - - +
64D LEU* 5.0 0.4 - - - +
74D THR* 1.3 74.3 - - - +
76D ILE* 1.3 59.6 + - - +
77D LEU* 4.0 11.8 + - + -
88D TYR* 3.6 35.2 - - + -
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Residues in contact with ILE 76 (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 PRO* 5.2 2.5 - - + -
18D VAL 3.3 7.6 - - - +
19D HIS* 3.7 41.3 - - + +
62D ALA* 3.0 7.7 - - - +
63D SER* 2.8 53.2 + - - +
65D ALA* 4.4 18.2 - - + -
74D THR* 4.0 9.6 - - + +
75D LEU* 1.3 76.1 - - - +
77D LEU* 1.3 68.4 + - - +
78D HIS* 3.6 16.4 + - + +
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Residues in contact with LEU 77 (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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16D GLU 4.4 0.2 - - - +
17D PRO* 3.2 3.1 - - - +
18D VAL* 2.8 46.5 + - + +
20D LEU* 4.3 11.2 - - + -
46D VAL* 5.2 0.2 - - + -
61D MET* 3.8 24.0 - - + +
62D ALA* 3.7 20.0 - - + -
75D LEU* 4.1 16.6 - - + -
76D ILE* 1.3 72.6 - - - +
78D HIS* 1.3 65.0 + - - +
79D ARG 3.4 3.3 + - - +
80D ALA* 5.0 6.1 - - + +
84D ASP* 4.4 14.1 - - + +
88D TYR* 3.7 27.8 - - + +
112D LEU* 3.9 21.8 - - + -
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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