Contacts of the helix formed by residues 102 - 119 (chain D) in PDB entry 3T79
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 ASP 102 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A GLN* 4.5 20.8 - - - +
193A SER* 6.1 0.5 - - - -
386A SER* 5.2 6.4 - - - +
388A GLU* 5.3 0.7 - - - +
100D GLU 3.3 4.8 + - - +
101D PHE* 1.3 86.9 - - - +
103D TYR* 1.3 60.1 + - - +
104D SER* 2.4 40.1 + - - -
105D ASN* 3.8 25.7 + - - +
309D LYS* 4.6 0.2 - - - +
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Residues in contact with TYR 103 (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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101D PHE* 3.5 17.5 + + - -
102D ASP* 1.3 69.5 + - - +
104D SER* 1.3 53.3 - - - +
105D ASN 2.6 18.1 + - - -
106D VAL* 3.2 24.6 - - + +
107D ILE* 3.1 30.7 + - + +
147D PHE* 4.3 14.0 + + - -
150D ASN* 4.6 2.3 + - - -
275D TRP* 5.6 5.8 - + - -
276D PRO* 3.5 20.0 - - + +
309D LYS* 3.3 54.8 - - + +
310D MET* 3.4 31.8 + - - +
312D ARG* 4.1 38.1 - - + -
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Residues in contact with SER 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ILE* 4.7 1.0 - - - +
111A GLN* 2.6 33.7 + - - -
102D ASP* 2.4 30.5 + - - -
103D TYR* 1.3 76.1 - - - +
105D ASN* 1.3 57.2 + - - +
107D ILE* 4.3 15.7 - - - +
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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
----------------------------------------------------------
111A GLN* 4.8 2.0 - - - +
192A GLN 5.1 2.9 - - - +
193A SER* 4.7 9.9 + - - -
386A SER* 3.1 28.6 + - - +
387A GLN* 4.2 8.8 + - - +
388A GLU* 4.7 2.2 - - - +
389A HIS* 2.1 68.0 + - + -
390A LEU* 4.4 10.9 - - - +
102D ASP* 3.9 26.4 - - - +
103D TYR 2.6 1.6 + - - -
104D SER* 1.3 83.1 + - - +
106D VAL* 1.3 62.6 + - - +
107D ILE 2.8 5.3 + - - -
108D ALA 3.7 3.5 + - - -
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Residues in contact with VAL 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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388A GLU* 4.8 5.5 + - + +
389A HIS* 3.2 11.8 - - + +
101D PHE* 3.9 12.6 - - + -
103D TYR* 3.2 49.6 - - + +
105D ASN* 1.3 75.0 - - - +
107D ILE* 1.3 62.5 + - - +
109D ILE* 2.9 25.1 + - + +
147D PHE* 3.3 22.1 - - + -
275D TRP* 3.0 39.5 - - + +
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Residues in contact with ILE 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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104A SER* 4.3 20.6 - - - +
107A ILE* 5.7 3.8 - - + -
108A ALA* 5.5 1.1 - - + -
111A GLN* 5.1 3.6 - - - +
103D TYR* 3.1 25.4 + - + +
104D SER* 4.3 14.8 - - - +
105D ASN 2.8 2.8 + - - +
106D VAL* 1.3 77.1 - - - +
108D ALA* 1.3 67.9 + - + +
109D ILE 2.8 6.4 + - - -
110D LEU* 2.9 22.2 + - + +
111D GLN* 3.0 33.1 + - + +
147D PHE* 4.4 5.6 - - + -
312D ARG* 4.7 24.0 - - + +
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Residues in contact with ALA 108 (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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108A ALA* 3.5 30.1 - - + -
111A GLN* 3.7 12.3 - - - +
389A HIS* 4.7 2.9 - - - +
393A GLN* 3.6 21.5 - - - +
105D ASN 3.7 2.4 + - - -
106D VAL 3.3 1.0 + - - -
107D ILE* 1.3 82.0 - - + +
109D ILE* 1.3 58.3 + - + +
111D GLN* 4.0 8.7 - - - -
112D LYS* 2.8 33.5 + - - +
261D LEU* 4.9 0.8 - - - +
393D GLN* 4.4 0.4 - - - +
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Residues in contact with ILE 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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389A HIS* 3.7 33.4 - - + +
392A ALA* 4.5 13.2 - - + -
393A GLN* 5.5 2.5 - - + +
105D ASN 4.0 1.8 - - - +
106D VAL* 2.9 30.7 - - + +
107D ILE 2.8 1.2 + - - -
108D ALA* 1.3 77.8 - - + +
110D LEU* 1.3 69.3 + - - +
112D LYS 3.9 0.2 - - - -
113D ILE* 3.0 39.5 + - + +
143D PHE* 4.3 7.4 - - + -
147D PHE* 4.8 2.5 - - + -
256D PHE* 4.6 8.1 - - + -
261D LEU* 3.8 28.7 - - + -
262D PRO* 6.1 0.2 - - + -
268D TRP* 4.7 10.3 - - + -
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Residues in contact with LEU 110 (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 ILE* 2.9 15.6 + - + +
109D ILE* 1.3 80.2 - - - +
111D GLN* 1.3 72.1 + - + +
113D ILE* 3.5 1.0 - - - +
114D SER* 2.9 19.8 + - - +
143D PHE* 3.6 23.2 - - + -
144D GLN* 4.5 18.6 - - + +
147D PHE* 3.5 51.0 - - + -
148D ASN* 5.7 0.7 - - - +
196D THR* 4.1 33.0 - - + +
312D ARG* 4.1 17.0 - - - +
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Residues in contact with GLN 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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104A SER* 2.8 36.4 + - - +
105A ASN* 4.4 1.0 + - - +
108A ALA* 3.7 8.1 - - - +
107D ILE* 3.0 34.0 + - + +
108D ALA* 4.0 2.7 - - - +
110D LEU* 1.3 86.8 - - + +
112D LYS* 1.3 56.5 + - - +
113D ILE 2.7 9.5 + - - -
114D SER* 3.0 9.2 + - - -
115D ILE* 3.3 16.3 + - - +
196D THR* 4.4 24.6 - - + +
389D HIS* 2.6 35.1 + - + -
390D LEU* 4.5 10.6 - - + +
393D GLN* 3.3 12.5 + - - +
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Residues in contact with LYS 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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112A LYS* 5.2 11.7 - - - +
393A GLN* 6.3 0.7 - - - +
108D ALA* 2.8 23.6 + - + +
109D ILE 4.0 1.8 - - - +
111D GLN* 1.3 69.5 - - - +
113D ILE* 1.3 52.4 + - - +
115D ILE* 3.5 4.2 - - - +
116D ASN* 2.2 43.4 + - - +
259D CYS* 2.3 36.8 + - + +
260D GLN* 4.6 6.4 + - - +
261D LEU* 3.8 28.0 - - + +
393D GLN* 2.7 57.0 + - + +
395D ILE* 4.8 9.9 - - - -
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Residues in contact with ILE 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 ILE* 3.0 20.6 + - + +
110D LEU 2.9 3.4 + - - +
111D GLN 2.7 4.2 + - - -
112D LYS* 1.3 71.8 - - - +
114D SER* 1.3 72.0 + - - +
115D ILE 3.1 2.0 - - - -
116D ASN* 2.9 17.5 + - - +
117D LEU* 2.9 30.4 + - + -
139D LEU* 6.0 0.2 - - + -
140D LEU* 4.5 4.7 - - + -
143D PHE* 3.0 45.5 - - + -
255D ILE* 4.4 12.3 - - + -
256D PHE* 3.6 24.2 - - + -
259D CYS* 4.2 13.6 - - + -
261D LEU* 4.0 12.6 - - + -
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Residues in contact with SER 114 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D LEU* 2.9 21.1 + - - -
111D GLN 4.0 1.6 - - - -
113D ILE* 1.3 72.8 - - - +
115D ILE* 1.3 53.8 + - - +
117D LEU* 2.9 3.7 + - - +
118D TRP* 2.8 39.9 + - - -
140D LEU* 2.9 22.3 - - - +
143D PHE* 5.9 0.6 - - - -
144D GLN* 2.1 37.6 + - - -
195D PHE* 3.1 14.9 + - - -
196D THR* 4.7 6.3 - - - -
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Residues in contact with ILE 115 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111D GLN 3.3 17.7 + - - +
112D LYS* 3.5 16.2 - - - +
113D ILE 2.9 0.8 + - - -
114D SER* 1.3 77.5 - - - +
116D ASN* 1.3 71.3 - - - +
118D TRP* 2.9 29.1 + - - +
119D ASN* 2.9 12.9 + - - +
195D PHE* 5.4 6.7 - - + +
196D THR* 6.2 0.2 - - - +
356D PHE* 4.1 10.6 - - + -
390D LEU* 2.7 39.7 - - + +
391D LEU* 3.0 30.5 - - + +
393D GLN* 4.6 3.4 - - + -
394D LEU* 3.7 18.6 - - + +
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Residues in contact with ASN 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 LYS* 2.2 39.2 + - - +
113D ILE 2.9 5.2 + - - +
115D ILE* 1.3 86.2 - - - +
117D LEU* 1.3 63.7 + - - +
119D ASN* 3.4 25.1 + - - +
122D THR* 4.6 9.4 - - - +
136D LYS* 4.8 0.2 - - - +
255D ILE* 5.0 1.5 - - + +
258D TYR* 4.3 8.1 - - + -
259D CYS* 3.9 17.8 - - - -
393D GLN 3.7 10.5 + - - -
394D LEU* 2.9 28.0 - - - +
395D ILE* 2.9 26.0 - - + +
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Residues in contact with LEU 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 ILE* 2.9 19.0 + - + +
114D SER 3.5 7.2 - - - +
116D ASN* 1.3 76.3 - - - +
118D TRP* 1.3 66.5 + - - +
125D LEU* 6.2 1.8 - - + -
130D PHE* 5.3 5.4 - - + -
136D LYS* 3.3 67.7 - - + +
137D LEU* 4.4 4.7 - - - +
139D LEU* 3.7 21.5 - - + -
140D LEU* 3.6 37.0 - - + +
143D PHE* 5.9 0.7 - - + -
255D ILE* 3.7 29.4 - - + -
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Residues in contact with TRP 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 SER 2.8 26.3 + - - -
115D ILE* 3.1 9.0 - - - +
117D LEU* 1.3 79.0 - - - +
119D ASN* 1.3 67.0 + - - +
120D PRO* 3.0 6.4 - - - +
133D CYS* 4.8 2.9 - - - +
137D LEU* 3.3 30.1 - - + -
140D LEU* 3.9 7.2 - - + +
195D PHE* 2.9 56.8 + + + +
200D PHE* 3.6 30.3 - + - -
201D THR* 3.1 40.8 - - + -
204D VAL* 4.1 12.3 - - + -
352D LEU* 4.4 9.2 - - + -
356D PHE* 3.5 17.5 - - + -
359D HIS* 3.8 31.2 + - - -
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Residues in contact with ASN 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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115D ILE 2.9 8.8 + - - +
116D ASN* 3.4 19.6 + - - +
118D TRP* 1.3 76.4 - - - +
120D PRO* 1.3 71.1 - - - +
121D SER* 2.7 35.0 + - - +
122D THR* 3.9 1.9 - - + +
136D LYS* 2.6 28.9 + - - -
258D TYR* 5.2 1.8 + - - -
356D PHE* 3.5 20.4 - - + -
394D LEU* 3.7 7.7 - - + +
396D ASP* 3.1 30.5 + - - +
398D THR* 3.2 10.0 - - - +
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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