Contacts of the strand formed by residues 130 - 135 (chain E) in PDB entry 3CF5
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 ARG 130 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E ASN* 4.3 20.3 + - + +
87E LEU 3.0 15.3 - - - +
88E GLU* 4.3 3.1 - - + +
89E LEU* 4.3 1.4 - - - +
125E VAL* 4.1 3.2 - - - +
126E PRO* 2.7 64.8 - - + +
127E GLU* 2.8 28.4 + - + +
129E THR* 1.3 81.9 - - - +
131E ILE* 1.3 60.7 + - - +
132E ASP* 4.2 16.8 + - - +
165E VAL* 6.1 3.1 - - + -
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Residues in contact with ILE 131 (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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86E ASN* 3.2 3.8 - - - +
87E LEU* 2.3 71.6 + - + +
88E GLU 6.2 0.2 - - - -
89E LEU* 4.1 14.6 - - + +
96E ALA* 4.0 9.9 - - + -
103E LEU* 3.2 33.0 - - + -
105E MET* 3.0 37.0 - - + -
123E PHE* 4.5 1.6 - - + -
124E ALA 4.0 5.8 - - - +
125E VAL* 5.3 2.7 - - + +
129E THR 4.3 0.2 - - - -
130E ARG* 1.3 72.2 + - - +
132E ASP* 1.3 74.4 + - - +
133E VAL* 4.2 4.3 - - + -
148E VAL* 3.8 10.8 - - + -
162E VAL* 5.5 1.3 - - + -
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Residues in contact with ASP 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E THR* 2.7 22.4 + - - -
85E ILE 3.5 2.7 - - - -
86E ASN* 2.5 24.5 - - - +
123E PHE* 3.6 2.4 - - - -
124E ALA* 2.9 54.6 + - + +
126E PRO* 5.0 5.2 - - + -
130E ARG* 4.2 13.8 + - - +
131E ILE* 1.3 81.1 - - - +
133E VAL* 1.3 67.1 + - - +
134E SER* 3.5 8.8 + - - -
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Residues in contact with VAL 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E THR* 3.6 2.5 - - - -
85E ILE 2.7 37.2 + - - +
87E LEU* 4.4 4.5 - - + -
121E VAL* 3.8 17.0 - - + -
122E THR 3.9 3.6 - - - +
123E PHE* 4.1 22.0 - - + -
131E ILE* 4.2 9.2 - - + -
132E ASP* 1.3 79.2 + - - +
134E SER* 1.3 62.1 + - - +
141E VAL* 2.8 29.1 - - + +
144E VAL* 4.9 3.4 - - + -
145E ALA* 3.8 35.9 - - + +
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Residues in contact with SER 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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82E GLY 5.5 0.2 - - - -
83E TYR 2.7 21.3 + - - -
84E THR* 3.1 17.8 + - - +
121E VAL* 3.2 22.7 - - - +
122E THR* 3.4 22.0 + - - +
124E ALA* 6.1 1.6 - - - -
132E ASP* 3.5 6.3 + - - -
133E VAL* 1.3 79.2 - - - +
135E GLY* 1.3 59.8 + - - +
141E VAL* 4.1 1.9 - - - +
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Residues in contact with GLY 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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82E GLY* 3.5 2.9 - - - -
83E TYR 2.5 47.3 + - - +
120E GLY 4.6 5.2 - - - -
121E VAL* 4.6 4.0 - - - -
122E THR* 5.0 1.8 + - - -
134E SER* 1.3 80.3 + - - +
136E ILE* 1.3 68.5 + - - -
137E ASP 4.0 0.4 - - - -
141E VAL* 3.8 11.4 - - - -
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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