Contacts of the strand formed by residues 128 - 134 (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 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ASP* 3.3 22.7 - - + +
57A ILE 4.8 0.7 - - - +
58A LEU* 4.2 32.1 - - + +
72A LYS* 6.2 5.2 - - + +
120A TYR* 3.6 8.6 - - - -
124A GLY* 3.5 0.3 - - - -
125A SER* 2.8 40.4 + - - +
126A ASP* 4.0 18.5 + - - +
127A GLY* 1.3 82.3 - - - +
129A LEU* 1.3 60.5 + - - +
130A VAL* 3.9 15.3 + - + +
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Residues in contact with LEU 129 (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* 5.3 0.2 - - + -
56A ASP 2.8 14.1 + - - +
57A ILE* 3.4 11.3 - - + +
58A LEU 3.1 20.6 + - - -
104A VAL* 4.6 6.3 - - + -
116A VAL* 3.6 33.0 - - + +
119A LEU* 3.8 34.8 - - + +
120A TYR* 3.9 15.0 - - + +
123A PHE* 3.9 22.4 - - + +
124A GLY* 4.5 0.4 - - - -
128A LYS* 1.3 73.1 - - - +
130A VAL* 1.3 67.0 + - - +
131A LEU* 3.6 32.4 + - + -
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Residues in contact with VAL 130 (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* 3.6 23.1 - - + +
60A LYS* 4.1 22.4 - - + +
103A TYR 4.1 3.5 - - - +
104A VAL* 4.5 6.2 - - - +
105A ASN 4.5 5.4 + - - -
123A PHE 5.3 1.8 + - - -
125A SER* 5.6 7.0 - - - +
128A LYS* 3.9 21.7 + - + +
129A LEU* 1.3 78.8 - - - +
131A LEU* 1.3 70.3 + - - +
132A HIS* 3.8 27.0 + - + +
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Residues in contact with LEU 131 (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* 4.0 11.2 - - + -
58A LEU 3.1 7.1 + - - -
59A LEU* 3.4 19.3 - - + +
60A LYS 3.0 23.6 + - - +
81A ILE* 4.6 7.6 - - + -
84A LEU* 3.6 31.6 - - + -
102A ILE* 4.2 20.2 - - + -
103A TYR 3.5 13.5 - - - +
104A VAL* 3.6 21.1 - - + -
116A VAL* 5.1 0.9 - - + -
129A LEU* 3.6 30.9 + - + +
130A VAL* 1.3 83.8 - - - +
132A HIS* 1.3 64.7 + - - +
133A TYR 4.0 0.5 + - - -
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Residues in contact with HIS 132 (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* 3.2 38.2 + - + +
61A ALA 5.0 1.0 + - - -
62A VAL* 4.0 25.1 - - + +
101A PHE 3.7 0.5 - - - +
102A ILE* 3.4 4.5 - - - -
103A TYR* 2.9 36.2 + - + +
105A ASN 5.6 0.9 - - - -
106A GLN* 3.3 51.6 + - + +
130A VAL* 3.8 21.5 - - + +
131A LEU* 1.3 77.4 - - - +
133A TYR* 1.3 59.1 + - - +
139A TRP* 4.3 12.6 - + + -
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Residues in contact with TYR 133 (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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59A LEU* 3.8 32.6 + - + -
60A LYS 3.0 36.4 + - - -
61A ALA* 3.3 18.0 + - + +
62A VAL* 3.1 25.9 + - - +
65A THR* 3.5 14.4 + - - -
66A PRO 3.4 20.0 - - - -
67A ILE* 3.5 4.3 - - - +
68A MET* 3.0 36.9 + - + +
71A LYS* 5.5 0.9 - - - -
88A ILE* 4.7 12.8 - - + -
92A LEU* 3.7 19.7 - - + -
100A LEU* 4.4 10.8 - - + -
101A PHE 3.3 8.1 - - - +
102A ILE* 4.6 10.8 - - + +
131A LEU 4.6 0.9 - - - -
132A HIS* 1.3 73.6 - - - +
134A CYS* 1.3 63.1 + - - +
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Residues in contact with CYS 134 (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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62A VAL* 3.4 32.8 - - + +
63A GLY 4.2 7.2 - - - -
65A THR* 3.6 8.7 - - - -
100A LEU* 3.6 5.0 - - - +
101A PHE* 2.7 39.8 + - - +
103A TYR* 4.8 6.3 - - + -
132A HIS 5.5 0.2 - - - -
133A TYR* 1.3 78.1 - - - +
135A LYS* 1.3 62.0 + - - +
136A SER* 3.2 37.9 + - - +
138A ALA* 4.4 12.3 - - + -
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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