Contacts of the helix formed by residues 139 - 146 (chain A) in PDB entry 2FV7
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 ALA 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A VAL* 4.2 22.2 - - + -
97A PHE* 3.7 24.9 - - + -
99A TYR* 4.5 0.2 - - - +
135A ASP 3.0 14.8 + - - +
136A LEU* 3.0 10.3 + - - +
138A ALA* 1.3 76.1 - - - +
140A ALA* 1.3 62.4 + - - +
141A ASN 3.3 2.7 - - - -
142A VAL* 3.1 13.7 - - + +
143A ILE* 3.0 25.6 + - + +
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Residues in contact with ALA 140 (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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136A LEU 2.9 8.6 + - - +
137A ARG* 3.1 21.7 + - + +
138A ALA 3.3 1.2 + - - -
139A ALA* 1.3 77.8 - - - +
141A ASN* 1.3 57.5 + - - +
143A ILE* 3.8 6.9 - - - +
144A SER* 2.9 33.0 + - - -
166A MET* 5.0 8.7 - - - -
115B ASN* 3.7 32.3 - - + +
116B GLU* 5.3 1.8 - - - +
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Residues in contact with ASN 141 (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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97A PHE* 6.2 2.2 - - + -
138A ALA 4.9 4.6 + - - +
139A ALA 3.3 1.0 - - - -
140A ALA* 1.3 74.3 - - - +
142A VAL* 1.3 61.2 + - - +
144A SER* 3.8 4.6 + - - -
145A ARG* 3.1 61.3 + - - +
33B SER* 3.1 27.2 + - - +
45B HIS* 5.5 1.4 + - - -
115B ASN* 1.9 35.7 + - - +
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Residues in contact with VAL 142 (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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16A ALA* 4.1 24.5 - - + +
19A VAL* 3.7 5.9 - - + +
70A SER* 4.1 17.9 - - - +
72A VAL* 4.2 12.6 - - + -
97A PHE* 3.7 34.9 - - + -
139A ALA* 3.1 23.3 + - + +
141A ASN* 1.3 75.4 - - - +
143A ILE* 1.3 73.8 + - - +
145A ARG* 3.5 10.8 + - - +
146A ALA* 3.2 20.8 + - - +
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Residues in contact with ILE 143 (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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19A VAL* 4.4 15.0 - - + -
21A VAL* 4.2 20.4 - - + -
136A LEU* 4.3 18.8 - - + +
139A ALA* 3.0 24.2 + - + +
140A ALA* 3.8 4.9 - - - +
142A VAL* 1.3 87.9 - - + +
144A SER* 1.3 64.6 + - - +
146A ALA* 3.2 18.0 + - - +
149A MET* 4.3 11.9 - - + -
163A ALA* 4.6 6.7 - - + +
166A MET* 4.2 27.6 - - + -
167A ALA* 4.0 29.2 - - + +
172A VAL* 3.5 7.4 - - - +
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Residues in contact with SER 144 (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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140A ALA 2.9 22.6 + - - -
141A ASN* 3.6 6.4 + - - -
143A ILE* 1.3 74.1 - - - +
145A ARG* 1.4 59.4 + - - +
146A ALA 3.4 1.6 - - - +
170A SER* 3.4 33.6 - - - +
172A VAL* 3.4 14.5 - - - +
45B HIS* 3.2 39.9 - - - -
46B LYS* 5.8 1.0 - - - +
115B ASN* 3.5 10.2 + - - -
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Residues in contact with ARG 145 (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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15A VAL* 4.2 27.8 - - + +
16A ALA 4.1 6.7 - - - +
17A ALA* 5.4 0.3 - - - -
141A ASN* 3.1 51.7 + - - +
142A VAL* 3.5 9.2 + - - +
143A ILE 3.3 0.4 - - - -
144A SER* 1.4 73.7 - - - +
146A ALA* 1.3 63.7 + - - +
147A LYS* 5.1 3.1 - - - +
33B SER* 5.1 7.5 + - - -
45B HIS* 3.8 35.7 + - + +
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Residues in contact with ALA 146 (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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16A ALA 3.5 9.4 - - - -
17A ALA 3.8 4.9 - - - +
19A VAL* 3.4 31.9 - - + -
142A VAL 3.2 2.4 + - - -
143A ILE 3.2 16.8 + - - +
144A SER 4.2 0.9 - - - +
145A ARG* 1.3 81.7 - - - +
147A LYS* 1.3 63.5 + - - +
148A VAL 3.9 9.9 - - - +
149A MET* 5.4 0.4 - - - -
172A VAL* 3.6 21.8 - - + +
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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