Contacts of the helix formed by residues 112 - 124 (chain A) in PDB entry 3RLQ
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLU* 4.8 3.1 - - - +
110A ILE* 3.8 3.0 + - - +
111A ALA* 1.3 79.9 - - - +
113A SER* 1.3 76.6 + - - +
114A GLY* 3.1 24.7 + - - +
115A THR* 3.3 19.5 + - - +
116A LYS* 4.4 1.0 + - - +
134A PHE 3.0 28.3 + - - -
135A GLY* 4.0 10.5 + - - -
136A VAL* 3.9 16.4 - - - +
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Residues in contact with SER 113 (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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112A LYS* 1.3 84.9 - - - +
114A GLY* 1.3 64.7 + - - +
115A THR 3.1 0.7 + - - -
116A LYS* 3.5 6.8 + - - +
117A ALA* 3.1 23.5 + - - +
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Residues in contact with GLY 114 (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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112A LYS* 3.1 15.5 - - - +
113A SER* 1.3 80.7 + - - +
115A THR* 1.3 57.7 + - - +
117A ALA* 3.8 8.5 - - - -
118A PHE* 2.9 31.4 + - - +
134A PHE* 3.6 31.3 - - - +
136A VAL* 4.5 1.5 - - - +
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Residues in contact with THR 115 (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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25A GLU* 3.5 40.8 - - + +
26A ILE* 3.8 20.8 - - + +
29A LEU* 4.3 13.3 - - + +
111A ALA* 4.5 1.7 - - - -
112A LYS* 3.5 23.4 + - - +
113A SER 3.1 0.8 - - - -
114A GLY* 1.3 79.9 - - - +
116A LYS* 1.3 63.4 + - - +
118A PHE* 3.4 4.6 + - - +
119A MET* 3.4 22.7 + - + +
136A VAL* 3.8 20.3 - - - +
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Residues in contact with LYS 116 (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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25A GLU* 3.9 29.6 + - + +
112A LYS 4.4 1.2 + - - +
113A SER* 3.5 7.2 + - - +
115A THR* 1.3 78.3 - - - +
117A ALA* 1.3 65.8 + - - +
119A MET* 3.2 14.9 + - + +
120A GLU* 3.0 48.5 + - + +
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Residues in contact with ALA 117 (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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113A SER* 3.1 20.3 + - - +
114A GLY* 3.8 3.8 - - - +
116A LYS* 1.3 79.0 - - - +
118A PHE* 1.3 56.5 + - - +
120A GLU* 3.2 16.4 + - - +
121A ALA* 2.9 27.7 + - - +
134A PHE* 3.7 21.4 - - + -
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Residues in contact with PHE 118 (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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29A LEU* 3.6 27.6 - - + -
33A ILE* 5.1 0.2 - - + -
114A GLY 2.9 20.5 + - - +
115A THR 3.7 3.1 - - - +
116A LYS 3.2 0.2 - - - -
117A ALA* 1.3 75.7 - - - +
119A MET* 1.3 61.2 + - - +
121A ALA* 3.0 5.8 + - + +
122A LEU* 3.0 57.0 + - + +
126A ALA* 6.0 0.7 - - + -
127A ASP 4.2 4.9 - - - -
128A ILE* 3.8 19.3 - - + -
131A ILE* 3.5 53.2 - - + -
134A PHE* 3.5 37.4 - + + -
136A VAL* 4.3 5.6 - - + -
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Residues in contact with MET 119 (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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25A GLU* 3.4 32.3 - - + +
28A GLN* 3.7 26.5 - - - +
29A LEU* 3.6 40.6 - - + -
32A LEU* 4.5 15.1 - - + +
115A THR* 3.4 17.7 + - + +
116A LYS* 3.2 12.0 + - + +
118A PHE* 1.3 76.5 - - - +
120A GLU* 1.3 62.4 + - - +
122A LEU* 3.4 9.2 + - - +
123A GLN* 3.1 29.2 + - + +
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Residues in contact with GLU 120 (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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116A LYS* 3.0 41.3 + - + +
117A ALA* 3.4 19.6 + - - +
119A MET* 1.3 74.3 - - - +
121A ALA* 1.3 60.3 + - - +
123A GLN* 3.2 9.0 + - - +
124A ALA* 2.9 29.2 + - - +
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Residues in contact with ALA 121 (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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117A ALA 2.9 13.8 + - - +
118A PHE* 3.0 10.5 + - + +
120A GLU* 1.3 77.9 - - - +
122A LEU* 1.3 60.9 + - - +
124A ALA* 3.0 15.3 + - - +
125A GLY 3.1 0.7 + - - -
126A ALA* 2.8 38.4 + - + +
134A PHE* 3.7 24.2 - - + -
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Residues in contact with LEU 122 (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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29A LEU* 5.3 0.2 - - + -
32A LEU* 3.8 29.2 - - + -
38A TYR* 4.4 13.9 - - + +
118A PHE* 3.0 47.1 + - + +
119A MET* 3.7 7.4 - - - +
121A ALA* 1.3 75.4 - - - +
123A GLN* 1.3 63.4 + - + +
125A GLY* 3.0 14.2 + - - -
126A ALA* 3.5 22.4 + - + +
127A ASP 3.7 3.8 - - - -
128A ILE* 3.7 30.1 - - + +
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Residues in contact with GLN 123 (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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32A LEU* 6.0 5.1 - - - +
119A MET* 3.1 20.6 + - + +
120A GLU* 3.5 10.5 - - - +
122A LEU* 1.3 77.8 - - + +
124A ALA* 1.3 58.3 + - - +
125A GLY* 3.2 1.1 + - - -
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Residues in contact with ALA 124 (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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120A GLU 2.9 16.2 + - - +
121A ALA* 3.0 10.0 + - - +
123A GLN* 1.3 76.0 - - - +
125A GLY* 1.3 57.9 + - - +
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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