Contacts of the strand formed by residues 139 - 145 (chain E) in PDB entry 4XCS
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 139 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E ALA* 3.8 17.7 - - + -
7E LYS 3.6 31.2 - - - +
8E ILE* 3.4 7.4 - - + +
9E GLY 2.9 29.1 + - - -
10E HIS 2.9 18.9 + - - +
11E PRO 5.8 0.2 - - - +
12E ALA* 4.2 8.0 - - + +
13E PRO* 5.0 5.8 - - + -
116E TYR* 5.3 1.1 - - + -
131E PHE* 3.9 17.5 - - + -
132E ILE 3.5 17.0 - - - +
133E ILE* 3.8 17.3 - - + +
137E GLY 3.9 1.4 + - - -
138E ILE* 1.3 72.8 - - - +
140E ARG* 1.3 59.4 + - - +
141E GLN 3.6 16.8 - - - +
142E ILE* 3.8 16.6 - - + -
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Residues in contact with ARG 140 (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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8E ILE* 3.6 5.8 - - - +
38E TYR* 3.5 7.7 + - + +
132E ILE* 2.8 19.4 + - + +
134E ASP* 3.2 30.0 + - + +
138E ILE* 3.5 18.6 - - - +
139E LEU* 1.3 76.9 - - - +
141E GLN* 1.3 57.9 + - - +
163E PHE* 3.6 39.0 + - + -
166E THR* 5.4 1.2 + - - -
167E ASP* 2.3 36.8 + - - -
145F ASN* 3.1 25.8 - - - +
146F ASP* 2.8 54.8 + - - +
148F PRO* 5.4 2.6 - - - +
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Residues in contact with GLN 141 (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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8E ILE* 3.7 1.1 - - - +
130E LEU* 4.1 10.1 - - - +
131E PHE* 3.3 6.4 - - - -
132E ILE* 3.0 38.6 + - + -
139E LEU* 3.6 6.4 - - - +
140E ARG* 1.3 80.8 - - - +
142E ILE* 1.3 73.2 + - - +
143E THR* 3.3 19.8 + - - +
159E LEU* 3.3 37.0 - - - +
163E PHE* 3.9 3.5 - - + -
143F THR* 4.0 8.5 - - + +
144F VAL 3.3 13.7 - - - +
145F ASN* 2.9 28.4 + - + -
151F ARG* 5.9 0.4 - - - +
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Residues in contact with ILE 142 (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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6E ALA* 4.1 21.1 - - + +
7E LYS* 4.5 0.4 - - - -
8E ILE* 3.9 16.6 - - + +
116E TYR 5.4 1.3 - - - +
130E LEU 3.4 3.8 - - - -
131E PHE* 3.8 18.6 - - + -
139E LEU* 3.8 28.0 - - + -
141E GLN* 1.3 78.5 - - - +
143E THR* 1.3 64.4 + - - +
144E VAL* 3.6 27.8 - - + +
1F MET* 4.2 18.2 - - + -
142F ILE* 3.6 1.2 - - + +
143F THR* 3.3 2.4 - - - -
144F VAL* 3.0 44.0 + - + +
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Residues in contact with THR 143 (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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128E ARG 3.7 0.3 - - - +
129E GLY* 3.1 5.5 - - - -
130E LEU* 2.8 50.7 + - - +
141E GLN* 3.3 20.4 + - - +
142E ILE* 1.3 71.5 - - - +
144E VAL* 1.3 66.6 + - - +
145E ASN* 4.3 1.8 - - - +
151E ARG* 3.8 23.6 + - - +
141F GLN* 3.8 20.4 - - + +
142F ILE 3.3 4.3 - - - +
143F THR* 2.8 25.6 + - - +
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Residues in contact with VAL 144 (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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116E TYR 5.4 0.4 - - - +
117E GLY 4.4 0.2 - - - +
118E VAL* 3.8 23.1 - - + -
127E PHE* 3.6 31.2 - - + -
128E ARG 3.4 3.8 - - - +
131E PHE* 4.9 0.2 - - + -
142E ILE* 3.6 21.1 - - + -
143E THR* 1.3 77.8 - - - +
145E ASN* 1.3 67.2 + - - +
0F HIS* 4.1 6.3 - - + -
1F MET* 3.9 19.5 - - + -
8F ILE* 3.5 20.7 - - + +
141F GLN* 3.2 1.6 - - - +
142F ILE* 2.8 38.7 + - + +
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Residues in contact with ASN 145 (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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127E PHE* 3.5 6.2 - - - +
128E ARG* 3.0 42.8 + - - +
143E THR* 4.3 2.6 - - - +
144E VAL* 1.3 77.4 - - - +
146E ASP* 1.3 60.8 + - - +
147E LEU* 3.1 35.3 + - - +
151E ARG* 4.2 18.0 + - - +
8F ILE* 4.0 8.1 - - - -
140F ARG 3.2 17.5 - - - +
141F GLN* 3.0 29.8 + - + +
159F LEU* 5.0 0.8 - - - +
163F PHE* 4.1 1.3 - - + -
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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