Contacts of the helix formed by residues 126 - 139 (chain D) in PDB entry 4LQL
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 SER 126 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D TRP* 4.4 0.9 - - - -
80D MET 3.7 19.0 - - - +
81D HIS* 3.8 7.2 - - - -
82D THR 5.4 0.2 - - - -
104D ALA* 5.5 0.5 - - - +
105D THR 2.2 36.5 + - - +
106D GLN* 3.8 16.1 + - - +
124D HIS 4.0 1.6 + - - -
125D GLN* 1.3 74.1 - - - +
127D ALA* 1.3 71.3 + - - +
128D HIS* 3.3 1.7 - - - -
129D GLY* 3.9 2.9 - - - +
130D ASP* 3.3 24.1 + - - +
333F TYR 5.4 1.4 + - - -
334F THR* 6.1 1.0 - - - +
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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
----------------------------------------------------------
104D ALA* 6.4 0.9 - - - -
126D SER* 1.3 81.9 + - - +
128D HIS* 1.3 57.0 + - - +
129D GLY 3.4 2.4 + - - -
130D ASP* 3.6 5.2 + - - +
131D ARG* 2.6 45.8 + - - +
332F ASP* 4.4 16.2 - - + +
333F TYR 5.4 0.8 + - - -
334F THR* 4.8 20.9 - - - +
335F LEU* 5.1 8.5 - - + +
344F ILE* 5.4 4.3 - - + -
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Residues in contact with HIS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PHE* 3.5 26.4 - + + +
121D MET* 4.5 11.7 - - + +
125D GLN* 3.1 43.5 + - + +
126D SER 3.3 0.4 - - - -
127D ALA* 1.3 77.1 - - - +
129D GLY* 1.3 57.0 + - - +
130D ASP 3.6 0.2 - - - -
131D ARG* 4.4 3.8 - - - +
132D GLU* 4.6 1.4 - - - +
331F GLU* 4.0 16.9 + - + -
332F ASP* 3.0 30.1 - - + +
333F TYR* 4.3 10.8 - - - -
446F HIS* 3.2 54.5 - + + +
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Residues in contact with GLY 129 (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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80D MET* 4.2 5.3 - - - +
82D THR 4.3 3.1 - - - -
83D PHE* 3.8 29.4 - - - -
84D SER* 3.4 20.4 + - - -
125D GLN 4.1 3.0 + - - -
126D SER* 3.6 5.9 + - - -
127D ALA 3.3 0.8 - - - -
128D HIS* 1.3 78.2 + - - +
130D ASP* 1.3 63.7 + - - +
131D ARG 3.5 0.7 - - - -
132D GLU* 3.7 6.1 - - - +
133D TYR* 3.5 11.4 + - - +
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Residues in contact with ASP 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D TRP* 6.5 0.4 - - + -
80D MET* 4.9 10.7 - - + +
102D HIS* 4.9 9.6 - - + -
103D LEU 5.6 0.9 - - - +
104D ALA* 4.2 26.9 - - + -
126D SER 3.3 19.1 + - - +
127D ALA* 3.9 4.3 - - - +
129D GLY* 1.3 76.4 - - - +
131D ARG* 1.3 54.1 + - + +
132D GLU 3.3 0.4 - - - -
133D TYR* 2.9 9.4 + - - +
134D ALA* 2.6 37.4 + - - +
440F MET* 4.8 3.6 - - + -
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Residues in contact with ARG 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D ALA* 2.6 53.6 + - - +
128D HIS* 4.0 1.4 - - - +
129D GLY 4.3 0.2 - - - +
130D ASP* 1.3 74.5 - - + +
132D GLU* 1.3 56.9 + - - +
134D ALA 3.7 1.2 - - - +
135D TYR* 3.0 25.6 + - - +
332F ASP* 4.7 19.4 + - - +
344F ILE* 5.1 7.3 - - - +
432F LEU* 5.3 4.8 - - - +
436F ALA* 3.2 30.3 - - - +
439F TRP* 3.5 25.2 - - - +
440F MET* 4.1 19.3 - - + +
444F GLY 3.1 17.0 - - - +
445F GLY* 3.1 35.1 - - - +
446F HIS* 4.3 7.0 - - + +
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Residues in contact with GLU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PHE* 3.7 23.1 - - + -
84D SER 4.1 8.2 - - - +
86D ALA* 2.9 37.5 + - - +
128D HIS 4.6 2.9 + - - +
129D GLY 3.7 12.6 + - - +
131D ARG* 1.3 77.9 - - - +
133D TYR* 1.3 62.5 + - - +
135D TYR* 3.6 15.3 + - - +
136D ILE 3.7 0.9 + - - -
188F VAL* 3.1 16.9 - - + +
189F ALA* 2.9 22.2 + - - +
190F VAL* 2.2 37.7 + - - -
445F GLY* 5.0 1.8 - - - -
446F HIS* 4.1 16.2 - - + +
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Residues in contact with TYR 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D THR* 5.0 5.8 - - - -
80D MET* 4.2 17.3 - - + -
84D SER* 4.6 3.1 - - - +
86D ALA* 4.2 7.8 - - + +
89D TRP* 4.5 26.7 - + + -
100D LEU* 6.0 4.5 - - + -
102D HIS* 5.0 13.2 - + + -
129D GLY 3.5 9.6 + - - +
130D ASP* 2.9 13.4 + - - +
132D GLU* 1.3 71.5 - - - +
134D ALA* 1.3 59.5 + - - +
135D TYR 3.0 4.5 - - - -
136D ILE* 2.8 31.2 + - + +
137D ASN* 2.9 14.5 + - + +
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Residues in contact with ALA 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D HIS* 4.9 12.5 - - + -
130D ASP 2.6 18.4 + - - +
131D ARG 3.4 3.8 + - - +
133D TYR* 1.3 73.0 - - - +
135D TYR* 1.3 59.2 + - - +
137D ASN* 3.7 10.6 - - + +
138D SER* 3.2 23.6 + - - -
146D SER* 5.8 1.8 - - - +
440F MET* 3.1 44.8 - - + +
443F GLY 4.5 0.2 - - - +
444F GLY 5.0 0.4 - - - -
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Residues in contact with TYR 135 (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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131D ARG 3.0 13.4 + - - +
132D GLU* 3.6 15.5 - - - +
133D TYR 2.9 1.4 + - - -
134D ALA* 1.3 72.8 - - - +
136D ILE* 1.3 60.3 + - + +
137D ASN 3.0 3.6 - - - -
138D SER* 2.8 5.6 + - - -
139D ARG* 2.6 52.7 + - + +
189F ALA* 4.9 13.5 - - + -
190F VAL* 5.1 10.3 - - - -
394F SER* 6.0 6.3 - - - -
396F PHE* 5.9 5.6 - + - -
443F GLY* 5.0 5.2 - - - -
444F GLY 4.5 8.7 - - - +
445F GLY* 5.7 1.8 - - - -
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Residues in contact with ILE 136 (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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196C VAL* 5.1 4.0 - - - +
200C ILE* 5.0 10.3 - - + -
86D ALA* 3.7 19.5 - - + +
87D LYS* 5.0 0.4 - - - -
89D TRP* 4.0 29.8 - - + +
90D ILE* 3.5 34.5 - - + -
93D THR* 5.1 8.2 - - - +
132D GLU 3.7 0.2 + - - -
133D TYR* 2.8 21.0 + - + +
135D TYR* 1.3 83.4 - - + +
137D ASN* 1.3 58.4 + - + +
138D SER 3.5 0.2 - - - -
139D ARG* 4.6 5.4 - - + +
140D LEU* 3.1 34.9 - - + +
142D VAL* 5.2 0.2 - - - +
189F ALA* 3.9 25.6 - - + -
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Residues in contact with ASN 137 (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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93D THR* 5.9 1.6 - - - +
100D LEU* 4.3 24.5 - - + -
102D HIS* 6.2 3.8 - - + -
133D TYR* 2.9 16.4 + - + +
134D ALA* 3.7 9.2 - - + +
135D TYR 3.0 0.2 - - - -
136D ILE* 1.3 81.3 - - + +
138D SER* 1.3 58.1 + - - +
140D LEU 4.2 1.1 - - - -
141D ASN* 3.7 0.9 + - - -
142D VAL* 3.3 37.7 + - + +
144D ALA* 4.6 11.6 - - + +
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Residues in contact with SER 138 (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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134D ALA 3.2 17.7 + - - -
135D TYR* 2.8 4.9 + - - -
137D ASN* 1.3 77.8 - - - +
139D ARG* 1.3 60.2 + - - +
140D LEU 3.1 2.0 - - - -
141D ASN* 2.9 23.8 + - - +
440F MET 4.7 0.2 - - - -
441F LYS* 3.4 24.9 - - - -
443F GLY* 4.7 8.1 - - - -
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Residues in contact with ARG 139 (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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194C ASP* 3.8 14.8 + - - -
196C VAL* 4.0 8.8 + - - +
197C ALA* 3.2 37.1 - - - +
200C ILE* 3.5 25.2 - - + +
135D TYR* 2.6 34.1 + - + +
136D ILE* 4.6 9.0 - - + +
138D SER* 1.3 73.1 - - - +
140D LEU* 1.3 58.3 + - - +
141D ASN* 3.2 1.6 + - - +
395F TYR* 3.0 22.0 + - - +
396F PHE* 3.8 17.3 - - + +
397F ASP* 3.1 40.3 - - - +
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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