Contacts of the strand formed by residues 120 - 128 (chain E) in PDB entry 3KC3
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 120 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52E LEU* 5.3 0.4 - - + -
105E VAL* 4.8 4.0 - - - +
108E HIS* 3.4 53.6 - - + +
109E TRP* 3.7 39.7 - - + +
112E SER* 2.8 13.6 + - - +
119E ARG* 1.3 82.8 + - - +
121E VAL* 1.3 63.2 + - - +
122E ASP* 4.0 6.5 - - - +
123E VAL* 3.8 27.1 - - + -
136E ILE* 3.6 22.7 - - + -
137E VAL 3.6 9.9 - - - +
138E MET* 4.4 1.6 - - + -
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Residues in contact with VAL 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E LEU* 6.2 0.2 - - - +
63E TYR* 4.6 5.8 - - - +
90E PHE* 3.6 35.2 - - + -
109E TRP* 5.1 5.3 - - - -
119E ARG* 4.4 20.4 - - - +
120E ILE* 1.3 75.9 - - - +
122E ASP* 1.3 77.5 + - + +
137E VAL* 2.8 14.2 + - + +
138E MET 4.1 0.4 - - - -
139E GLU* 3.7 21.5 - - + +
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Residues in contact with ASP 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E LEU* 5.8 2.6 - - - +
53E GLN 5.0 4.0 - - - +
55E LYS* 2.8 46.2 + - + +
63E TYR* 4.3 8.3 + - - +
120E ILE* 4.0 2.0 - - - +
121E VAL* 1.3 94.0 - - - +
123E VAL* 1.3 64.9 + - - +
124E TYR* 3.7 21.7 + - + -
136E ILE 3.6 0.2 - - - -
137E VAL* 2.6 45.2 + - + +
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Residues in contact with VAL 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E LEU* 4.0 23.5 - - + +
53E GLN 4.4 1.1 + - - +
54E ILE* 3.1 23.8 - - + +
55E LYS* 2.9 24.5 + - - +
105E VAL* 4.0 33.9 - - + -
120E ILE* 3.8 20.2 - - + -
122E ASP* 1.3 79.8 + - - +
124E TYR* 1.3 71.0 + - - +
134E LEU* 4.3 9.0 - - + -
135E LEU 3.3 8.1 - - - +
136E ILE* 4.5 10.5 - - + -
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Residues in contact with TYR 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E ILE* 3.8 2.0 - - - -
55E LYS* 3.3 35.4 - - + +
57E ASN* 3.2 43.1 - - - -
59E ILE* 3.5 36.3 - - + -
62E ASP* 2.7 22.8 + - - +
63E TYR* 3.6 10.6 + + - -
122E ASP* 3.7 15.6 + - + -
123E VAL* 1.3 78.3 - - - +
125E GLU* 1.3 59.5 + - - +
126E ASN* 3.8 14.6 - - - +
134E LEU* 3.5 4.0 - - - -
135E LEU* 2.8 38.5 + - + +
137E VAL* 3.6 24.2 - - + -
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Residues in contact with GLU 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E ILE* 3.4 17.6 - - + +
55E LYS 2.8 12.3 + - - +
56E LYS* 2.6 38.8 - - + +
102E ARG* 3.0 24.7 + - - +
124E TYR* 1.3 70.3 - - - +
126E ASN* 1.3 70.5 + - - +
132E LYS* 3.1 40.8 + - + +
133E CYS 3.3 8.5 - - - +
134E LEU* 4.3 5.6 - - + -
51F GLY* 3.5 18.2 + - - -
52F LEU 4.1 8.2 + - - +
106F GLU* 5.8 0.2 - - - +
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Residues in contact with ASN 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E LYS 3.7 2.6 + - - -
57E ASN 2.9 25.2 + - - -
58E ALA* 3.8 3.8 - - - -
59E ILE* 2.8 32.4 + - - +
124E TYR* 3.8 13.7 - - - +
125E GLU* 1.3 95.8 + - - +
127E LEU* 1.3 61.4 + - - +
128E TYR* 5.9 0.2 - - + -
132E LYS* 3.6 5.3 - - - +
133E CYS* 2.8 37.5 + - + +
135E LEU* 3.9 11.5 - - + +
48F VAL* 3.0 22.2 - - + +
49F LYS 3.5 8.1 - - - +
50F SER* 4.3 1.5 - - - +
51F GLY* 4.2 4.9 - - - +
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Residues in contact with LEU 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E ASN* 1.3 73.4 - - - +
128E TYR* 1.3 60.4 + - - +
129E ALA 4.3 0.2 - - - -
130E GLY* 3.7 28.9 - - - +
131E ARG 3.7 6.7 - - - +
132E LYS* 3.9 18.2 - - + -
47F HIS 4.0 1.0 - - - +
48F VAL* 3.6 3.3 - - - -
49F LYS* 2.8 46.1 + - + +
50F SER 3.8 13.5 - - - +
51F GLY* 6.1 1.3 - - - -
106F GLU* 4.9 2.0 - - - +
109F TRP* 4.3 15.9 - - + +
110F ARG* 3.9 31.9 - - + +
113F GLN* 4.3 20.2 - - + +
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Residues in contact with TYR 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A HIS 5.2 5.2 + - - -
271A ILE* 6.1 1.2 - - - +
273A PRO* 3.9 26.1 - - + +
94E MET* 4.4 18.2 - - + -
126E ASN* 4.1 1.0 + - + -
127E LEU* 1.3 76.0 - - - +
129E ALA* 1.3 80.4 + - + +
130E GLY 2.9 0.7 + - - -
131E ARG* 3.0 21.7 + - - +
133E CYS* 4.0 20.6 - - + -
135E LEU* 6.0 0.2 - - + -
45F GLN 5.4 1.4 + - - -
46F PHE* 4.5 21.3 - + - -
47F HIS* 3.7 27.6 - - + -
48F VAL* 3.5 26.5 - - + -
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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