Contacts of the helix formed by residues 128 - 133 (chain V) in PDB entry 3A0B
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 PRO 128 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C GLU* 3.4 42.5 - - + +
79C LYS* 4.4 4.5 - - - +
80C PRO* 5.1 6.1 - - + -
61V TYR* 4.7 1.2 + - - -
125V ASP 2.9 12.5 - - - +
127V PHE* 1.3 84.4 - - + +
129V LYS* 1.3 55.1 + - + +
130V MET 2.6 18.3 + - - +
131V ARG* 2.7 52.3 + - + +
132V ASN* 4.1 3.6 + - - -
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Residues in contact with LYS 129 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C GLU 4.0 1.3 + - - -
79C LYS* 4.7 5.2 - - + -
80C PRO* 4.1 19.1 - - + -
83C GLU* 3.9 21.5 - - - +
394C GLU* 4.7 7.0 - - - -
61V TYR* 3.5 59.5 + - + +
62V ALA* 3.7 21.0 + - - +
65V SER* 4.6 10.8 - - - +
119V PRO* 4.9 6.1 - - - +
127V PHE* 2.7 36.6 + - - +
128V PRO* 1.3 75.6 - - - +
130V MET* 1.3 54.1 + - + +
132V ASN* 4.5 1.7 + - - +
133V LEU* 2.8 25.5 - - - +
1041V HEM 4.1 11.1 - - - +
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Residues in contact with MET 130 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62V ALA* 5.1 11.2 - - - +
102V MET* 4.2 21.1 - - + +
119V PRO* 3.8 31.2 - - + +
120V SER* 3.3 39.5 - - - +
121V LEU* 3.7 29.6 - - + +
123V SER* 5.0 7.6 - - - +
125V ASP* 5.9 0.7 - - - -
126V ILE 5.1 0.4 - - - +
127V PHE 4.0 6.5 - - - +
128V PRO* 2.6 7.5 + - + -
129V LYS* 1.3 76.9 - - + +
131V ARG* 1.3 63.0 + - - +
132V ASN 3.3 2.7 - - - -
133V LEU* 3.0 34.6 + - + +
1041V HEM 5.2 9.0 - - + -
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Residues in contact with ARG 131 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C GLU* 3.4 27.6 + - - +
104C GLU* 3.3 28.3 + - - +
121V LEU* 5.0 6.3 - - - +
125V ASP* 2.9 58.0 + - + +
128V PRO* 2.7 45.9 + - + +
130V MET* 1.3 72.3 - - - +
132V ASN* 1.3 69.7 + - - +
133V LEU 4.1 1.6 - - - +
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Residues in contact with ASN 132 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ILE* 4.9 2.2 - - - +
77C PRO* 3.5 31.4 - - - +
78C GLU* 5.0 2.4 + - - +
61V TYR* 3.4 25.0 + - + +
128V PRO 4.1 4.2 + - - -
129V LYS 5.0 0.2 - - - +
130V MET 3.3 0.8 - - - -
131V ARG* 1.3 82.9 - - - +
133V LEU* 1.3 76.1 - - + +
134V THR* 4.4 2.9 - - - -
137V ASP* 4.9 0.7 - - - -
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Residues in contact with LEU 133 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58V LEU* 3.9 19.7 - - + -
61V TYR* 5.4 1.6 - - + -
62V ALA* 4.8 6.3 - - + -
102V MET* 5.5 0.7 - - + -
121V LEU* 4.6 11.0 - - + +
129V LYS 2.8 29.8 - - - +
130V MET* 3.0 39.9 - - + +
131V ARG 4.1 3.1 - - - +
132V ASN* 1.3 87.8 - - + +
134V THR* 1.3 59.7 + - - +
137V ASP* 3.3 13.9 - - + -
138V LEU* 3.3 32.3 - - + -
141V ILE* 3.8 16.6 - - + -
1041V HEM 5.9 0.7 - - + -
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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