Contacts of the strand formed by residues 128 - 135 (chain E) in PDB entry 6I53
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 LEU 128 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A TYR* 3.1 12.7 + - - -
113D THR* 3.7 33.0 - - + -
62E TYR* 3.3 2.6 - - - -
63E PHE* 2.7 47.5 + - + +
65E GLN* 6.1 0.2 - - - +
106E VAL* 4.2 17.9 - - + -
112E LYS* 5.6 0.7 - - - -
113E ASN 3.7 4.9 - - - +
114E ARG* 3.7 19.1 - - + -
126E TYR* 3.6 40.8 - - + +
127E GLY* 1.3 79.7 - - - +
129E ARG* 1.3 57.9 + - - +
130E ILE* 3.8 21.3 - - + -
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Residues in contact with ARG 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE* 3.7 19.7 - - - +
101A PHE 3.2 25.1 + - - +
102A HIS 3.7 11.3 + - - -
103A ASN* 4.2 0.8 - - - +
104A GLY* 3.2 28.2 + - - +
160A TYR* 3.6 8.6 + - + -
45E ALA* 5.6 3.0 - - - +
60E THR* 4.7 14.0 - - + +
61E MET 3.4 10.3 - - - +
62E TYR* 3.7 26.5 + - + +
106E VAL* 3.7 3.4 - - - +
107E HIS* 3.1 70.9 + - + +
109E VAL 5.9 0.2 + - - -
113E ASN* 3.7 28.5 + - + +
128E LEU* 1.3 73.2 - - - +
130E ILE* 1.3 60.0 + - - +
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Residues in contact with ILE 130 (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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112D MET* 3.7 42.8 - - + -
113D THR* 4.0 8.1 - - + -
59E LEU 3.5 2.6 - - - +
60E THR* 3.4 2.0 - - - -
61E MET* 3.1 41.6 + - + +
63E PHE* 3.9 19.3 - - + -
98E PHE* 4.3 10.1 - - + -
104E SER* 4.4 1.1 - - - -
105E PHE 3.9 2.9 - - - -
106E VAL* 4.3 5.4 - - + -
107E HIS* 4.6 0.2 - - - -
128E LEU* 3.8 33.8 - - + -
129E ARG* 1.3 76.0 - - - +
131E THR* 1.3 70.8 + - - +
132E THR* 3.9 13.9 + - - +
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Residues in contact with THR 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LYS* 4.5 3.5 + - - +
48E ASP* 4.4 2.5 - - - +
58E THR* 3.8 22.2 - - + -
59E LEU 3.3 3.4 - - - +
60E THR* 3.1 26.1 + - - +
103E LYS 4.0 1.2 - - - +
104E SER* 3.4 18.4 - - - -
105E PHE* 3.3 40.4 + - + -
107E HIS* 2.4 32.1 + - + -
129E ARG 4.1 0.6 + - - -
130E ILE* 1.3 70.7 - - - +
132E THR* 1.3 60.0 + - - +
133E THR* 5.1 1.0 + - - +
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Residues in contact with THR 132 (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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58E THR* 3.4 3.1 - - - +
59E LEU* 2.7 60.4 + - + +
61E MET* 4.7 12.8 - - + -
98E PHE* 4.7 8.1 - - + +
101E ASP* 3.0 25.3 + - - +
104E SER* 3.7 12.6 - - - -
130E ILE* 3.8 7.2 - - + +
131E THR* 1.3 74.9 - - - +
133E THR* 1.3 65.0 + - - +
134E ALA* 3.8 5.7 + - - +
152E LEU* 4.4 20.4 - - + +
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Residues in contact with THR 133 (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 ASP* 3.4 30.3 - - + +
57E TYR 3.4 10.3 - - - +
58E THR* 3.8 21.1 + - - +
101E ASP* 4.2 0.2 + - - -
102E LYS* 3.0 31.4 + - + +
103E LYS* 3.2 29.6 + - + +
131E THR* 5.1 1.0 + - - +
132E THR* 1.3 74.7 + - - +
134E ALA* 1.3 60.1 + - - +
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Residues in contact with ALA 134 (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 ASP* 3.3 2.6 - - - +
57E TYR* 2.8 71.0 + - + +
100E ASN* 3.3 23.3 - - + -
101E ASP* 4.7 0.7 - - - +
132E THR* 3.7 7.3 + - + +
133E THR* 1.3 73.9 - - - +
135E ALA* 1.3 59.0 + - - +
151E THR 4.3 0.4 - - - +
152E LEU* 4.1 16.4 - - + -
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Residues in contact with ALA 135 (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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187D ARG* 3.8 26.5 - - + +
55E MET 3.7 7.2 - - - +
56E ASP* 4.0 1.6 - - - +
57E TYR* 4.6 1.4 - - - -
100E ASN* 3.1 34.2 + - + +
102E LYS* 3.8 24.7 - - - -
134E ALA* 1.3 74.9 - - - +
136E CYS* 1.3 70.0 + - - +
137E MET* 6.4 0.9 - - + -
151E THR* 4.9 2.3 + - - +
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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