Contacts of the strand formed by residues 54 - 61 (chain A) 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 LYS 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LYS* 1.3 82.6 - - - +
55A ILE* 1.3 69.6 + - - +
74A ALA* 3.8 34.8 + - + +
75A VAL 3.4 16.2 - - - +
76A GLU* 3.6 28.9 - - - +
77A ARG* 4.0 4.9 + - - -
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Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LYS* 1.3 74.0 - - - +
56A ASP* 1.3 65.5 + - - +
57A ILE* 3.8 7.4 + - + +
73A TRP 3.6 0.7 - - - +
74A ALA* 3.6 1.5 - - - -
75A VAL* 2.9 41.1 + - - +
77A ARG* 3.4 41.5 - - + +
116A VAL* 3.5 32.3 - - + -
117A GLY* 3.7 14.6 - - - +
120A TYR* 3.6 44.6 - - + -
129A LEU* 5.3 0.9 - - + -
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Residues in contact with ASP 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ILE* 1.3 78.1 - - - +
57A ILE* 1.3 59.0 + - - +
73A TRP 3.5 8.2 - - - +
74A ALA* 4.5 9.7 - - - +
120A TYR* 4.6 0.2 - - - -
127A GLY 3.5 24.0 + - - +
128A LYS* 3.3 12.5 - - + +
129A LEU* 2.8 32.2 + - - +
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Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ILE* 4.3 4.9 - - + +
56A ASP* 1.3 79.4 - - - +
58A LEU* 1.3 62.6 + - - +
59A LEU* 3.7 28.7 - - + -
71A LYS 3.2 5.5 - - - +
72A LYS* 3.5 2.6 - - - -
73A TRP* 2.9 37.8 + - + +
75A VAL* 3.5 31.2 - - + -
84A LEU* 3.8 18.8 - - + -
116A VAL* 3.5 31.2 - - + -
128A LYS* 5.3 0.4 - - - -
129A LEU* 3.4 15.0 - - + +
131A LEU* 4.0 11.7 - - + -
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ASP 4.2 0.8 + - - -
57A ILE* 1.3 71.9 - - - +
59A LEU* 1.3 66.2 + - - +
60A LYS* 3.7 32.3 + - + +
71A LYS* 3.6 21.8 - - + +
72A LYS* 4.0 27.6 - - + +
128A LYS* 4.2 32.7 - - + +
129A LEU 3.1 8.9 + - - +
130A VAL* 3.6 13.6 - - + +
131A LEU 3.1 25.4 + - - +
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ILE* 3.7 25.6 - - + -
58A LEU* 1.3 72.7 - - - +
60A LYS* 1.3 63.3 + - - +
61A ALA 4.4 0.2 + - - -
68A MET* 3.9 22.0 - - + -
70A THR 4.8 0.2 - - - +
71A LYS* 3.0 42.6 + - - +
73A TRP* 3.9 23.8 - - + +
84A LEU* 5.0 5.6 - - + -
87A PHE* 5.2 2.5 - - + -
88A ILE* 3.8 33.4 - - + -
102A ILE* 5.8 0.9 - - + -
131A LEU* 3.4 20.0 - - + +
133A TYR* 3.8 17.9 + - + -
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Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 3.8 27.8 - - + +
59A LEU* 1.3 79.5 - - - +
61A ALA* 1.3 61.5 + - - +
71A LYS* 5.9 0.9 - - - +
130A VAL* 4.1 19.2 - - + +
131A LEU 3.0 6.6 + - - +
132A HIS* 3.2 40.8 + - + +
133A TYR* 3.0 29.6 + - - -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LYS* 1.3 75.7 - - - +
62A VAL* 1.3 64.2 + - - +
63A GLY 4.0 2.0 + - - +
65A THR* 3.9 4.7 - - - +
67A ILE* 3.8 28.3 - - + -
71A LYS* 6.4 0.2 - - - +
132A HIS* 5.0 0.7 + - - -
133A TYR* 3.3 34.7 + - + +
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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