Contacts of the strand formed by residues 55 - 61 (chain D) in PDB entry 4GDK
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 ILE 55 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D LYS* 1.3 76.9 - - - +
56D ASP* 1.3 76.3 + - - +
57D ILE* 3.5 7.5 + - + -
74D ALA* 3.6 1.5 - - - -
75D VAL* 2.8 38.4 + - - +
77D ARG* 3.7 37.5 - - + +
116D VAL* 3.7 33.7 - - + -
117D GLY* 4.0 4.5 - - - -
120D TYR* 3.6 48.2 - - + -
129D LEU* 4.3 3.8 - - + -
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Residues in contact with ASP 56 (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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54D LYS* 4.1 4.0 + - - +
55D ILE* 1.3 74.3 - - - +
57D ILE* 1.3 60.8 + - - +
72D LYS* 5.6 13.9 - - + -
73D TRP 3.6 3.8 - - - +
74D ALA* 3.9 19.8 - - - +
120D TYR* 6.0 0.4 - - - -
127D GLY 3.9 20.5 + - - +
128D LYS* 3.2 12.4 - - + +
129D LEU 2.9 24.9 + - - -
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Residues in contact with ILE 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ILE* 3.9 9.4 - - + -
56D ASP* 1.3 76.0 - - - +
58D LEU* 1.3 63.2 + - - +
59D LEU* 3.7 28.3 - - + -
71D LYS 3.5 2.3 - - - +
72D LYS* 3.7 4.0 - - - +
73D TRP* 2.8 46.2 + - + +
75D VAL* 3.6 25.8 - - + -
84D LEU* 4.0 12.6 - - + -
116D VAL* 3.6 34.8 - - + -
128D LYS* 5.5 0.7 - - - -
129D LEU* 3.5 22.7 - - + +
131D LEU* 4.1 6.5 - - + -
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Residues in contact with LEU 58 (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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56D ASP 4.2 0.6 + - - -
57D ILE* 1.3 74.0 - - - +
59D LEU* 1.3 64.5 + - - +
60D LYS* 3.6 32.3 - - + +
71D LYS* 3.5 28.5 - - + +
72D LYS* 4.5 13.9 - - + +
128D LYS* 4.1 31.2 - - + +
129D LEU 3.2 6.3 + - - +
130D VAL* 3.5 14.6 - - + +
131D LEU* 2.9 25.6 + - - +
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Residues in contact with LEU 59 (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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57D ILE* 3.7 23.8 - - + -
58D LEU* 1.3 74.3 - - - +
60D LYS* 1.3 64.8 + - - +
68D MET* 4.0 14.6 - - + -
70D THR 4.8 0.2 - - - +
71D LYS* 2.8 44.9 + - - +
73D TRP* 3.7 27.8 - - + +
84D LEU* 5.6 3.8 - - + -
87D PHE* 5.2 3.1 - - + -
88D ILE* 3.7 32.3 - - + -
102D ILE* 6.0 0.2 - - + -
131D LEU* 3.4 23.3 - - + +
133D TYR* 3.7 15.8 - - + -
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Residues in contact with LYS 60 (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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58D LEU* 3.6 30.6 - - + +
59D LEU* 1.3 77.3 - - - +
61D ALA* 1.3 62.7 + - - +
71D LYS* 5.6 2.2 - - + -
128D LYS* 5.9 0.4 - - - +
130D VAL* 4.0 20.0 - - + +
131D LEU 3.0 7.9 + - - +
132D HIS* 3.2 42.0 + - + +
133D TYR* 2.9 29.8 + - - -
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Residues in contact with ALA 61 (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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60D LYS* 1.3 76.3 - - - +
62D VAL* 1.3 66.8 + - - +
63D GLY 4.1 1.0 + - - +
65D THR* 4.7 4.5 - - - +
66D PRO 4.6 0.7 - - - +
67D ILE* 3.6 30.5 - - + +
71D LYS* 6.1 1.6 - - - +
132D HIS* 4.9 0.5 + - - -
133D TYR* 3.4 35.9 + - + +
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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