Contacts of the helix formed by residues 112 - 125 (chain K) in PDB entry 6LTJ
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 PRO 112 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27J TYR* 3.3 21.5 - - + +
34J LYS* 4.5 4.0 - - - +
111J VAL 3.8 17.9 - - - +
112J LYS* 4.6 16.6 - - + +
110K LEU 3.3 9.8 - - - +
111K ASN* 1.3 100.8 - - - +
113K LYS* 1.3 66.9 + - - +
114K ALA* 3.3 5.4 - - + +
115K ASN* 3.2 33.5 + - - +
116K ARG* 3.5 5.9 + - - +
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Residues in contact with LYS 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J GLY* 3.6 29.8 + - - -
14J LEU* 6.2 0.4 - - - -
27J TYR* 3.3 39.7 + - + +
118J HIS* 4.3 21.5 - - - -
111K ASN 3.8 0.4 + - - -
112K PRO* 1.3 73.8 - - - +
114K ALA* 1.3 63.6 + - + +
116K ARG* 3.4 2.8 + - - +
117K GLU* 3.0 31.4 + - - +
371K HIS* 3.2 40.4 + - + +
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Residues in contact with ALA 114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J TYR* 4.8 0.4 + - - +
112K PRO* 3.3 5.2 - - + +
113K LYS* 1.3 85.8 - - + +
115K ASN* 1.3 65.7 + - - +
117K GLU* 3.4 16.9 + - - +
118K LYS* 2.9 29.6 + - - +
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Residues in contact with ASN 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K TRP* 3.2 41.1 - - + +
111K ASN* 3.2 21.5 - - - +
112K PRO* 3.2 27.2 + - - +
114K ALA* 1.3 82.0 - - - +
116K ARG* 1.3 59.3 + - - +
118K LYS* 5.8 0.4 - - - +
119K MET* 2.9 32.9 + - + +
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Residues in contact with ARG 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107K GLU* 2.5 35.3 + - - +
109K PRO 5.3 2.4 + - - -
111K ASN* 4.4 12.2 + - - +
112K PRO 3.5 8.6 + - - +
113K LYS* 3.4 8.2 + - - +
114K ALA 3.4 0.4 - - - -
115K ASN* 1.3 74.6 - - - +
117K GLU* 1.3 63.8 + - - +
119K MET* 3.2 14.0 - - + +
120K THR* 3.0 27.6 + - - +
133K TYR* 5.7 3.0 + - - -
134K VAL* 3.9 22.9 - - + +
136K ILE* 4.3 14.5 - - - +
370K VAL* 3.8 25.7 + - + -
371K HIS* 3.5 27.2 + - + +
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Residues in contact with GLU 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K LYS* 3.0 22.4 + - - +
114K ALA* 3.5 18.2 - - - +
116K ARG* 1.3 75.8 - - - +
118K LYS* 1.3 57.4 + - - +
120K THR* 2.3 26.9 + - - -
121K GLN* 3.0 41.7 + - - +
367K PRO* 4.2 15.1 - - + +
368K SER* 5.4 3.4 - - - +
370K VAL* 4.6 5.8 - - - -
371K HIS* 4.5 8.5 + - + +
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Residues in contact with LYS 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79K TRP* 3.5 60.5 - - + +
114K ALA 2.9 18.4 + - - +
115K ASN* 3.3 0.6 + - - +
117K GLU* 1.3 77.9 - - - +
119K MET* 1.3 59.0 + - - +
121K GLN* 3.3 9.7 + - + +
122K ILE* 2.9 38.2 + - + +
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Residues in contact with MET 119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79K TRP* 3.7 15.4 - - + -
82K MET* 6.3 1.3 - - - -
86K TRP* 4.8 13.8 - - + -
105K LEU* 3.8 25.0 - - + +
106K THR 5.8 0.4 - - - +
107K GLU* 3.8 19.5 - - + +
111K ASN* 4.0 14.4 - - - +
115K ASN* 2.9 22.9 + - + +
116K ARG* 3.2 16.8 - - + +
118K LYS* 1.3 77.8 - - - +
120K THR* 1.3 59.8 + - + +
122K ILE* 3.4 10.1 - - + +
123K MET* 2.9 32.1 + - - +
132K MET* 5.2 0.4 - - + -
134K VAL* 3.8 28.3 - - + -
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Residues in contact with THR 120 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116K ARG* 3.0 14.5 + - + +
117K GLU* 2.3 31.4 + - - -
119K MET* 1.3 78.2 - - + +
121K GLN* 1.3 56.6 + - - -
123K MET* 3.3 1.0 + - - +
124K PHE* 2.9 43.7 + - + +
132K MET* 3.8 25.8 - - + -
134K VAL* 5.6 0.7 - - + -
367K PRO* 3.3 21.4 + - - +
370K VAL* 3.7 32.8 - - + -
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Residues in contact with GLN 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117K GLU* 3.0 43.3 + - - +
118K LYS* 3.3 9.5 + - + +
120K THR* 1.3 75.7 + - - +
122K ILE* 1.3 58.4 + - - +
125K GLU* 2.9 39.1 + - + +
126K THR* 3.6 5.0 + - - -
362K TYR* 4.4 13.9 + - - +
367K PRO* 3.4 28.6 - - + +
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Residues in contact with ILE 122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79K TRP* 4.9 10.5 - - + +
82K MET* 6.5 0.9 - - + -
83K GLU* 3.7 39.3 - - + +
86K TRP* 5.1 11.0 - - + -
118K LYS* 2.9 30.5 + - + +
119K MET* 3.4 14.8 - - + +
121K GLN* 1.3 76.8 - - - +
123K MET* 1.3 66.3 + - + +
126K THR* 3.4 31.7 - - + +
127K PHE* 3.3 21.7 + - - +
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Residues in contact with MET 123 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K VAL* 5.8 1.1 - - + -
86K TRP* 3.6 36.1 - - + -
90K PHE* 5.6 4.5 - - + -
103K VAL* 4.5 9.2 - - + -
105K LEU* 3.8 21.3 - - + -
119K MET 2.9 18.8 + - - +
120K THR 4.0 1.8 - - - +
122K ILE* 1.3 81.6 - - + +
124K PHE* 1.3 52.6 + - - +
127K PHE* 3.2 35.0 - - + +
128K ASN* 2.6 28.6 + - - -
129K THR* 3.6 24.5 + - - +
132K MET* 4.2 19.5 - - + -
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Residues in contact with PHE 124 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120K THR* 2.9 24.3 + - + +
123K MET* 1.3 79.1 - - - +
125K GLU* 1.3 67.2 + - - +
126K THR 3.3 1.3 - - - -
128K ASN* 2.9 34.2 + - - +
129K THR* 3.2 28.7 - - - -
130K PRO 4.5 2.0 - - - -
132K MET* 3.5 37.0 - - + -
357K ILE* 4.1 8.7 - - + -
358K SER* 3.8 28.7 - - - -
359K LYS* 4.4 6.3 - - + -
362K TYR* 3.4 53.6 - + + -
369K ILE* 6.0 0.7 - - + -
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Residues in contact with GLU 125 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121K GLN* 2.9 23.8 + - + +
124K PHE* 1.3 76.4 - - - +
126K THR* 1.3 62.6 + - - +
128K ASN* 5.6 0.3 - - - +
362K TYR* 3.2 29.2 + - + +
363K ASP* 5.3 6.0 - - - +
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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