Contacts of the helix formed by residues 124 - 128 (chain D) in PDB entry 3V81
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 PHE 124 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D VAL* 4.1 26.2 - - + +
12D LEU* 3.3 30.5 - - + -
80D LEU* 4.7 16.2 - - + -
84D THR* 3.5 14.8 - - - -
120D LEU* 3.9 16.4 - - + -
121D ASP* 2.9 25.0 + - + +
123D ASP* 1.3 77.4 - - - +
125D ARG* 1.3 58.2 + - - +
126D LYS 3.1 3.1 - - - -
127D TYR* 2.8 47.3 + + + +
128D THR* 4.2 6.3 + - + -
153D TRP* 2.9 50.5 - + - -
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Residues in contact with ARG 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D THR* 4.9 4.0 - - - +
119D PRO* 4.1 9.3 - - - +
120D LEU* 2.8 44.8 + - + +
121D ASP 3.3 11.0 - - - +
122D GLU* 3.4 38.1 + - - +
124D PHE* 1.3 73.1 - - - +
126D LYS* 1.3 62.8 + - - +
127D TYR 2.9 0.4 - - - -
128D THR* 2.9 22.3 + - - -
145D GLN* 3.4 25.6 - - - +
146D TYR 3.4 19.3 - - - +
147D ASN* 3.1 45.0 + - - +
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Residues in contact with LYS 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LYS* 6.0 4.9 - - - +
54D ASN* 3.2 20.9 + - - +
56D TYR* 2.9 45.0 + - + +
122D GLU 4.7 1.9 + - - +
123D ASP 3.6 19.5 - - - +
125D ARG* 1.3 77.6 - - - +
127D TYR* 1.3 89.5 + - + +
128D THR 3.5 0.4 + - - -
129D ALA* 4.0 1.8 - - - +
145D GLN* 3.4 14.7 + - - +
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Residues in contact with TYR 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 3.7 27.1 - - + +
17D ASP* 3.7 2.0 + - - -
18D GLY* 3.4 32.5 - - - -
19D PRO* 3.7 11.8 - - + +
56D TYR* 3.4 37.4 + + - +
58D THR* 4.2 3.8 + - - -
80D LEU* 3.6 29.0 - - + +
123D ASP 4.1 6.7 - - - -
124D PHE* 2.8 42.8 + + + +
126D LYS* 1.3 108.8 + - + +
128D THR* 1.3 57.3 + - - +
129D ALA* 3.2 8.1 + - - +
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Residues in contact with THR 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D THR* 5.0 0.7 - - - -
77D PHE* 4.4 12.8 - - + -
80D LEU* 4.3 15.5 - - + -
120D LEU* 4.4 12.1 - - + -
124D PHE* 4.8 10.8 - - + +
125D ARG* 2.9 11.9 + - - +
127D TYR* 1.3 79.0 - - - +
129D ALA* 1.3 63.3 + - - +
130D PHE* 3.4 17.8 + - - +
145D GLN* 4.2 2.9 - - - -
146D TYR* 2.9 49.8 + - + +
150D PRO* 4.2 17.3 - - + -
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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