Contacts of the helix formed by residues 124 - 130 (chain D) in PDB entry 2IHU
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 ASP 124 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131C PRO* 4.3 16.7 + - + +
108D GLN* 4.8 1.1 - - - +
116D PRO* 3.7 27.2 - - + +
117D ASN* 5.2 1.2 + - - -
123D LEU* 1.3 69.3 - - - +
125D SER* 1.3 61.8 + - - +
126D VAL* 4.0 5.4 + - - +
127D ALA* 3.4 28.3 + - + +
128D ILE* 3.1 27.4 + - - +
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Residues in contact with SER 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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82D GLY 5.2 3.1 + - - -
85D MET* 3.6 28.9 - - - +
106D ALA* 5.9 0.2 - - - -
107D ALA 4.9 4.5 + - - -
108D GLN* 3.5 12.8 + - - +
123D LEU* 2.9 13.1 + - - +
124D ASP* 1.3 71.5 + - - +
126D VAL* 1.3 58.7 + - - +
128D ILE* 3.3 1.3 + - - +
129D VAL* 2.9 35.2 + - - +
165D PHE* 3.8 25.1 - - - -
167D SER* 4.1 12.8 + - - -
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Residues in contact with VAL 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D ASP* 3.4 5.9 + - - +
125D SER* 1.3 75.8 - - - +
127D ALA* 1.3 55.4 + - - +
130D ALA* 2.8 43.4 + - + +
136D ALA* 3.8 23.1 - - + +
137D VAL* 3.6 34.5 - - - +
138D GLU* 3.7 16.2 - - + +
165D PHE* 4.4 8.3 - - + -
167D SER* 4.2 8.5 - - - -
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Residues in contact with ALA 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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127C ALA 3.9 6.6 - - - +
131C PRO* 3.7 17.8 - - + +
124D ASP* 3.2 32.5 + - - +
126D VAL* 1.3 79.1 - - - +
128D ILE* 1.3 57.5 + - - +
130D ALA* 4.4 3.7 - - - +
131D PRO* 3.2 24.4 - - - +
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Residues in contact with ILE 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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89C SER* 5.8 0.7 - - - +
128C ILE* 3.7 49.5 - - + +
131C PRO* 3.8 13.5 - - + -
132C MET* 3.8 35.9 - - + -
85D MET* 4.0 22.2 - - + -
86D THR* 4.9 1.8 - - + -
89D SER* 5.4 7.0 - - - +
123D LEU* 4.0 20.2 - - + -
124D ASP 3.1 25.4 + - - +
125D SER* 3.7 4.7 - - - +
127D ALA* 1.3 77.4 - - - +
129D VAL* 1.3 60.7 + - + +
131D PRO* 3.5 7.4 - - - +
132D MET* 4.3 2.6 - - - +
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Residues in contact with VAL 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D MET* 3.8 25.6 - - + -
89D SER* 4.9 6.7 - - - -
92D ILE* 4.0 26.9 - - + -
125D SER 2.9 19.4 + - - +
128D ILE* 1.3 77.7 - - + +
130D ALA* 1.3 66.0 + - - +
131D PRO* 3.3 3.1 - - - -
132D MET* 3.0 18.3 + - + +
133D SER* 2.8 23.5 + - - +
136D ALA* 4.8 0.2 - - + -
165D PHE* 3.5 42.6 - - + -
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Residues in contact with ALA 130 (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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126D VAL* 2.8 29.0 + - + +
127D ALA* 4.4 3.6 - - - +
129D VAL* 1.3 73.1 - - - +
131D PRO* 1.4 66.1 - - + +
132D MET 3.1 1.0 + - - -
133D SER* 3.4 23.0 + - - +
136D ALA* 4.0 12.4 - - + +
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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