Contacts of the helix formed by residues 112 - 121 (chain D) in PDB entry 1F5Q
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 LYS 112 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42C GLU* 3.5 20.2 - - + +
100D HIS* 4.5 1.1 - - - -
110D PRO 4.6 6.5 - - - +
111D ILE* 1.3 76.8 - - - +
113D ALA* 1.3 64.3 + - - +
114D THR* 3.9 17.0 - - - +
115D GLN* 3.1 26.9 + - + +
116D LEU* 3.0 22.2 + - - +
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Residues in contact with ALA 113 (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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41C THR 5.4 0.7 - - - +
42C GLU* 2.9 20.3 + - - +
100D HIS* 4.0 16.6 + - + +
111D ILE 3.7 1.0 + - - -
112D LYS* 1.3 68.3 - - - +
114D THR* 1.3 58.8 + - + +
116D LEU* 3.1 7.7 + - - +
117D ALA* 2.7 36.2 + - - +
126D ALA* 3.5 28.9 - - + +
129D LEU* 3.9 9.1 - - + +
130D LEU* 4.5 11.7 - - + -
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Residues in contact with THR 114 (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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41C THR* 5.3 13.2 - - + -
42C GLU* 5.6 0.9 - - - +
112D LYS* 3.9 15.0 - - + +
113D ALA* 1.3 77.2 - - + +
115D GLN* 1.3 63.8 + - - +
117D ALA* 3.6 5.4 + - - +
118D TYR* 3.2 20.1 + - - +
126D ALA* 3.8 20.4 - - + +
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Residues in contact with GLN 115 (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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63D LEU* 3.6 34.3 - - + +
111D ILE* 4.9 1.5 - - + +
112D LYS* 3.1 38.0 + - + +
113D ALA 3.1 0.6 - - - -
114D THR* 1.3 80.0 + - - +
116D LEU* 1.3 64.8 + - - +
118D TYR* 2.9 13.3 + - + +
119D LEU* 2.9 37.0 + - + +
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Residues in contact with LEU 116 (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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55D TRP* 4.3 11.4 - - + -
59D VAL* 4.1 22.0 - - + -
96D ALA* 3.6 26.7 - - + +
99D LEU* 4.3 13.5 - - + -
100D HIS* 3.8 24.7 - - + +
111D ILE* 3.5 34.8 - - + -
112D LYS 3.0 10.7 + - - +
113D ALA* 3.6 6.3 - - - +
115D GLN* 1.3 75.5 - - - +
117D ALA* 1.3 52.8 + - - +
119D LEU* 3.2 8.0 + - + +
120D CYS* 2.7 38.4 + - - +
129D LEU* 4.1 12.6 - - + -
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Residues in contact with ALA 117 (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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113D ALA 2.7 20.3 + - - +
114D THR* 3.7 6.7 - - - +
116D LEU* 1.3 72.6 - - - +
118D TYR* 1.3 57.0 + - - +
120D CYS* 3.7 2.0 - - - +
121D GLY* 3.0 21.3 + - - -
124D THR* 3.8 17.4 - - - +
125D THR* 3.5 15.9 - - - +
126D ALA 3.5 25.4 - - - +
129D LEU* 3.6 12.2 - - + +
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Residues in contact with TYR 118 (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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114D THR 3.2 12.4 + - - +
115D GLN* 2.9 16.4 + - + +
117D ALA* 1.3 75.5 - - - +
119D LEU* 1.3 98.2 + - + +
120D CYS 2.9 2.6 + - - -
121D GLY* 3.0 14.9 + - - -
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Residues in contact with LEU 119 (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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55D TRP* 4.3 22.5 + - + +
59D VAL* 4.1 32.1 - - + -
63D LEU* 4.8 8.3 - - + -
115D GLN* 2.9 33.8 + - + +
116D LEU* 3.8 9.6 - - + +
118D TYR* 1.3 99.2 - - + +
120D CYS* 1.3 62.8 + - - +
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Residues in contact with CYS 120 (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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55D TRP* 3.9 7.2 - - - -
92D GLN* 3.5 46.3 - - + +
93D SER* 4.7 3.4 - - - -
96D ALA* 3.8 25.4 - - - -
116D LEU 2.7 21.1 + - - +
117D ALA* 3.7 7.0 - - - +
119D LEU* 1.3 81.4 - - - +
121D GLY* 1.3 60.9 + - - +
122D GLY 4.2 0.2 + - - -
124D THR* 4.2 17.0 - - + +
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Residues in contact with GLY 121 (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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117D ALA 3.0 7.7 + - - -
118D TYR* 3.0 14.4 + - - -
120D CYS* 1.3 81.1 - - - +
122D GLY* 1.3 65.8 + - - -
124D THR* 2.8 28.8 + - - -
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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