Contacts of the helix formed by residues 100 - 117 (chain D) in PDB entry 1AX4
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 GLY 100 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D GLN* 1.4 71.0 - - - +
101D ARG* 1.3 55.7 + - - +
103D ALA* 3.1 6.8 + - - +
104D GLU* 2.9 31.0 + - - +
261D THR* 5.1 1.4 - - - -
262D MET 3.8 8.5 - - - -
263D SER* 3.7 20.1 - - - +
266D LLP 2.8 35.1 + - - -
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Residues in contact with ARG 101 (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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72C TYR* 3.0 21.0 + - - -
293C VAL* 2.8 47.0 + - - +
294C PRO 3.3 19.2 - - - +
295C MET 4.1 7.6 - - - +
296C GLU 4.4 0.4 - - - +
297C GLY* 3.5 21.0 - - - +
298C PHE* 3.9 2.0 - - - +
99D GLN* 3.3 18.0 - - + +
100D GLY* 1.3 73.8 - - - +
102D GLY* 1.3 61.2 + - - +
104D GLU* 3.4 18.1 + - - +
105D ASN* 3.0 28.1 + - - +
132D PHE* 5.2 2.6 - - - -
134D THR* 3.5 29.2 - - - +
138D HIS* 3.5 6.0 + - - +
266D LLP 2.6 42.6 + - - +
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Residues in contact with GLY 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C MET 4.4 2.2 - - - -
97D ALA* 4.0 5.8 - - - -
98D HIS* 4.1 8.8 - - - -
99D GLN 3.0 9.6 + - - -
101D ARG* 1.3 79.8 - - - +
103D ALA* 1.4 63.5 + - - +
105D ASN* 3.3 7.1 + - - +
106D ILE* 3.1 26.7 + - - +
296D GLU* 3.4 26.1 - - - +
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Residues in contact with ALA 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ALA* 3.6 11.3 - - + +
99D GLN 3.1 7.4 + - - +
100D GLY* 3.1 10.4 + - - +
102D GLY* 1.4 76.9 - - - +
104D GLU* 1.3 61.2 + - - +
106D ILE* 3.4 3.7 + - - +
107D LEU* 3.0 26.2 + - - +
261D THR* 4.1 11.4 - - + +
262D MET 4.4 2.2 - - - +
275D LEU 3.6 20.6 - - - +
276D VAL* 3.4 26.1 - - + +
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Residues in contact with GLU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D GLY 2.9 16.6 + - - +
101D ARG* 3.5 10.4 - - - +
102D GLY 3.3 0.2 - - - -
103D ALA* 1.3 74.9 - - - +
105D ASN* 1.3 59.4 + - - +
108D PHE* 2.9 59.5 + - + +
134D THR* 2.7 29.0 + - - +
135D THR* 2.6 38.4 + - - +
138D HIS* 3.7 15.3 - - + -
223D ASP* 3.8 3.5 - - - +
261D THR* 4.5 11.7 + - - -
266D LLP 3.2 16.4 + - - -
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Residues in contact with ASN 105 (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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105C ASN* 4.2 2.0 - - - +
295C MET* 3.5 34.9 + - - +
101D ARG 3.0 17.3 + - - +
102D GLY* 3.6 7.9 - - - +
104D GLU* 1.3 77.4 - - - +
106D ILE* 1.3 55.7 + - - +
109D PRO* 3.2 13.0 - - - +
138D HIS* 3.6 18.3 + - + -
142D ASN* 5.7 0.5 + - - -
291D ARG* 2.8 47.3 + - - -
295D MET* 3.6 34.6 - - - +
296D GLU* 5.0 4.4 + - - -
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Residues in contact with ILE 106 (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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95D ILE* 4.2 13.9 - - + -
96D PRO 4.3 0.2 - - - +
97D ALA* 4.3 13.5 - - + -
102D GLY 3.1 15.5 + - - +
103D ALA* 3.6 7.9 - - - +
104D GLU 3.2 0.2 - - - -
105D ASN* 1.3 77.7 - - - +
107D LEU* 1.3 64.7 + - - +
109D PRO* 4.1 0.3 - - - +
110D VAL* 3.4 21.5 - - - +
276D VAL* 4.2 13.7 - - + -
288D ALA* 3.7 32.5 - - + +
291D ARG* 3.7 14.8 - - - +
292D CYS* 4.1 27.8 - - + +
295D MET* 5.2 3.1 - - + -
296D GLU* 3.6 28.7 - - + -
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Residues in contact with LEU 107 (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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103D ALA 3.0 14.0 + - - +
106D ILE* 1.3 84.2 - - + +
108D PHE* 1.3 69.6 + - + +
110D VAL* 3.1 7.3 + - + +
111D LEU* 3.0 32.4 + - + +
219D PHE* 5.4 0.2 - - + -
221D VAL* 4.1 25.8 - - + -
259D ALA* 4.4 13.5 - - + -
260D LEU 4.7 0.9 - - - +
261D THR* 3.8 22.4 - - + -
276D VAL* 4.5 19.3 - - + -
278D ILE* 4.7 5.8 - - + -
284D ILE* 3.9 27.6 - - + -
288D ALA* 4.7 6.3 - - + -
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Residues in contact with PHE 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D GLU* 2.9 34.2 + - + +
107D LEU* 1.3 77.7 - - + +
109D PRO* 1.3 66.0 - - + +
111D LEU* 2.9 19.6 + - + +
112D LEU* 3.1 12.9 + - - +
126D PHE* 4.1 25.5 - + + -
135D THR* 3.5 38.8 - - + -
138D HIS* 4.1 22.9 - - + +
139D VAL* 4.1 18.6 - - + -
142D ASN* 4.9 6.5 - - + +
188D VAL* 4.2 14.6 - - + -
221D VAL* 4.4 17.3 - - + -
261D THR* 4.3 21.1 - - + -
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Residues in contact with PRO 109 (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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104D GLU 3.6 2.0 - - - +
105D ASN* 3.2 29.4 - - - +
106D ILE 4.1 1.1 - - - +
107D LEU 3.6 1.6 - - - -
108D PHE* 1.3 95.4 - - + +
110D VAL* 1.3 54.5 + - - +
112D LEU* 3.3 7.1 + - + +
113D LYS* 3.0 29.7 + - - +
138D HIS* 6.0 0.2 - - - +
142D ASN* 3.6 33.8 - - - +
291D ARG* 3.5 30.5 - - - +
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Residues in contact with VAL 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D ILE 3.4 17.7 - - - +
107D LEU* 3.1 12.0 + - + +
109D PRO* 1.3 78.3 - - - +
111D LEU* 1.3 57.1 + - - +
113D LYS* 3.4 9.4 + - + +
114D TYR* 3.0 27.2 + - - +
284D ILE* 4.0 27.8 - - + +
287D LEU* 3.6 51.9 - - + +
288D ALA* 3.8 4.3 - - + +
291D ARG* 4.3 11.7 - - + -
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Residues in contact with LEU 111 (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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107D LEU* 3.0 35.1 + - + +
108D PHE* 2.9 18.3 + - + +
110D VAL* 1.3 73.7 - - - +
112D LEU* 1.3 66.3 + - - +
114D TYR* 3.4 6.4 + - + +
115D LYS* 3.1 24.4 + - - +
126D PHE* 4.6 2.5 - - + -
185D VAL* 3.6 17.7 - - + +
186D ALA* 4.1 11.0 - - + -
219D PHE* 3.7 33.7 - - + -
221D VAL* 3.6 29.6 - - + -
284D ILE* 4.1 21.1 - - + -
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Residues in contact with LEU 112 (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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108D PHE 3.1 10.2 + - - +
109D PRO* 3.5 9.6 - - + +
111D LEU* 1.3 76.6 - - - +
113D LYS* 1.3 64.7 + - - +
115D LYS* 3.1 4.2 + - - +
116D GLN* 3.0 51.4 + - + +
121D ALA* 4.3 1.6 - - + -
124D PRO* 3.8 30.1 - - + -
126D PHE* 5.4 1.1 - - + -
142D ASN* 3.3 39.7 - - + +
144D CYS* 4.0 5.8 - - - -
185D VAL* 3.5 18.9 - - + +
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Residues in contact with LYS 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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109D PRO 3.0 16.9 + - - +
110D VAL* 3.9 9.0 - - + +
112D LEU* 1.3 75.0 - - - +
114D TYR* 1.3 57.6 + - - +
116D GLN* 3.2 15.2 + - - +
117D LYS* 2.8 39.4 + - + +
287D LEU* 3.9 33.3 - - + +
290D GLN* 5.0 4.2 + - - -
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Residues in contact with TYR 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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110D VAL 3.0 18.3 + - - +
111D LEU* 3.6 7.9 - - + +
112D LEU 3.2 0.2 - - - -
113D LYS* 1.3 76.9 - - - +
115D LYS* 1.3 64.7 + - + +
117D LYS* 3.6 27.3 + - + +
118D GLU* 3.6 31.3 + - - -
219D PHE* 5.6 7.4 - + + -
281D ASN* 3.4 20.3 + - - -
283D GLU* 3.6 38.9 + - + -
284D ILE* 3.4 32.5 - - + -
287D LEU* 4.4 9.8 - - + +
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Residues in contact with LYS 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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111D LEU 3.1 18.4 + - - +
112D LEU 3.6 4.3 - - - +
114D TYR* 1.3 80.6 - - + +
116D GLN* 1.3 60.8 + - - +
117D LYS 3.7 0.2 + - - -
118D GLU* 3.6 19.5 + - - +
120D LYS* 3.3 31.6 + - + +
121D ALA* 3.7 20.4 - - + -
181D ALA 2.8 27.2 + - - -
182D ASP* 3.4 17.2 - - - +
184D ILE 2.9 22.7 + - - +
185D VAL* 4.4 17.4 + - + +
216D HIS 5.2 1.4 + - - -
217D GLY 4.2 16.2 + - - -
218D ILE* 4.3 6.7 - - - +
219D PHE 5.4 0.4 - - - +
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Residues in contact with GLN 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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112D LEU* 3.0 36.9 + - + +
113D LYS* 3.6 18.6 - - - +
115D LYS* 1.3 73.4 - - - +
117D LYS* 1.3 58.1 + - - +
118D GLU 3.1 2.5 - - - -
119D GLY* 2.7 25.3 + - - -
120D LYS 3.7 10.9 - - - +
121D ALA* 3.8 23.9 + - + +
124D PRO* 5.4 2.0 - - - +
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Residues in contact with LYS 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 LYS* 2.8 31.5 + - + +
114D TYR* 3.7 23.4 - - + +
115D LYS 3.4 0.6 - - - -
116D GLN* 1.3 72.1 - - - +
118D GLU* 1.3 72.1 + - + +
119D GLY* 3.2 0.9 + - - -
283D GLU* 3.4 26.6 + - - +
287D LEU* 3.9 23.2 - - - +
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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
------------------------------------------------------------
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