Contacts of the helix formed by residues 124 - 133 (chain A) in PDB entry 3WHD
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 THR 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A GLN* 4.9 5.1 + - - +
122A ILE* 3.7 6.4 - - - +
123A SER* 1.3 89.1 - - - +
125A GLU* 1.3 62.9 + - - +
126A ALA* 3.5 11.0 + - - +
127A GLU* 3.1 31.2 + - - +
128A GLN 3.2 9.5 + - - -
166A ARG* 4.8 7.4 - - - +
168A PHE* 4.0 7.0 - - - -
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Residues in contact with GLU 125 (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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124A THR* 1.3 70.6 - - - +
126A ALA* 1.3 59.5 + - - +
128A GLN* 3.3 7.5 + - + +
129A ASN* 2.8 51.7 + - - +
166A ARG* 5.1 9.4 + - - +
168A PHE* 3.5 33.2 - - + -
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Residues in contact with ALA 126 (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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91A PHE* 3.6 20.2 - - + -
92A GLN* 4.9 7.6 - - - +
124A THR* 3.1 10.8 + - - +
125A GLU* 1.3 78.2 - - - +
127A GLU* 1.3 58.7 + - - +
129A ASN* 3.4 9.2 + - - +
130A PHE* 3.0 28.8 + - - +
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Residues in contact with GLU 127 (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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91A PHE* 3.6 16.8 - - + -
92A GLN* 5.5 1.1 - - - +
94A ASN* 4.5 2.9 + - - -
96A TYR* 2.6 24.0 + - + +
120A MET* 4.0 10.1 - - + +
121A THR 3.3 10.2 - - - +
122A ILE* 4.3 1.8 - - + -
123A SER* 2.9 31.6 + - - +
124A THR* 3.1 19.9 + - - +
126A ALA* 1.3 79.3 - - - +
128A GLN* 1.3 62.6 + - - +
130A PHE* 3.3 5.9 + - - +
131A ILE* 3.2 22.2 + - - +
208A LYS* 2.5 31.6 + - - -
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Residues in contact with GLN 128 (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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122A ILE* 3.5 29.5 - - + +
124A THR 3.2 5.8 + - - +
125A GLU* 3.3 11.3 + - + +
127A GLU* 1.3 79.3 - - - +
129A ASN* 1.3 65.5 + - - +
130A PHE 3.2 0.2 + - - -
131A ILE* 3.2 7.3 + - - +
132A ILE* 3.0 44.4 + - + +
168A PHE* 3.8 26.9 - - + +
185A LEU* 3.7 10.4 - - + +
192A TRP* 3.7 21.4 + - - +
193A ALA* 4.6 0.4 - - - +
194A TRP* 2.8 30.8 + - - -
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Residues in contact with ASN 129 (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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125A GLU* 2.8 48.6 + - - +
126A ALA* 3.7 7.2 - - - +
128A GLN* 1.3 75.4 + - - +
130A PHE* 1.3 62.8 + - - +
132A ILE* 3.4 29.1 - - - +
133A GLN* 3.6 12.0 + - - +
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Residues in contact with PHE 130 (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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89A ARG* 3.8 16.4 - - + -
90A ALA 3.2 29.6 - - - -
91A PHE* 3.6 41.7 - + + -
96A TYR* 3.9 22.4 - + - -
126A ALA 3.0 14.2 + - - +
127A GLU 3.4 9.2 - - - +
128A GLN 3.1 0.2 - - - -
129A ASN* 1.3 77.0 - - - +
131A ILE* 1.3 73.3 + - + +
133A GLN* 3.1 43.5 + - - +
134A PHE* 3.3 29.7 - + - -
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Residues in contact with ILE 131 (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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89A ARG* 5.3 1.1 - - + -
96A TYR* 3.7 33.2 - - + -
98A PRO* 4.3 14.1 - - + -
120A MET* 3.8 26.7 - - + -
127A GLU 3.2 5.3 + - - +
128A GLN* 3.4 11.7 - - - +
130A PHE* 1.3 90.8 - - + +
132A ILE* 1.3 66.2 + - - +
134A PHE* 3.0 22.1 + - + +
135A LEU* 3.5 10.0 - - + +
185A LEU* 3.9 24.5 - - + -
206A ILE* 4.0 28.7 - - + -
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Residues in contact with ILE 132 (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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128A GLN* 3.0 33.1 + - + +
129A ASN* 3.4 35.4 - - + +
131A ILE* 1.3 75.4 - - - +
133A GLN* 1.3 63.0 + - + +
134A PHE 3.0 2.1 + - - -
135A LEU* 3.1 24.9 + - + +
185A LEU* 4.0 15.0 - - + -
192A TRP* 3.6 54.0 + - + +
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Residues in contact with GLN 133 (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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129A ASN 3.6 10.6 - - - +
130A PHE* 3.1 39.6 + - - +
131A ILE 3.1 0.6 + - - -
132A ILE* 1.3 81.9 - - + +
134A PHE* 1.3 88.9 + - + +
135A LEU 3.5 1.8 + - - +
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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