Contacts of the helix formed by residues 106 - 119 (chain A) 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 VAL 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A PHE* 4.0 11.9 - - + -
102A ASP 4.9 0.2 + - - -
103A TYR* 2.6 54.5 + - + +
105A ASN* 1.3 74.7 - - - +
107A ILE* 1.3 63.5 + - + +
109A ILE* 3.0 24.8 + - + +
110A LEU 3.8 1.2 + - - -
147A PHE* 3.2 19.5 - - + -
275A TRP* 3.0 37.7 - - + +
388D GLU* 5.5 5.1 + - + +
389D HIS* 3.5 11.5 - - + +
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Residues in contact with ILE 107 (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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103A TYR* 2.7 58.8 - - + +
104A SER* 3.7 11.7 - - - +
105A ASN 2.8 3.0 + - - -
106A VAL* 1.3 80.3 - - + +
108A ALA* 1.3 57.1 + - + +
110A LEU* 2.9 25.5 + - + +
111A GLN* 2.9 44.5 + - + +
147A PHE* 4.3 5.8 - - + -
312A ARG* 3.7 31.6 - - - +
104D SER* 4.7 1.3 - - - +
107D ILE* 5.7 4.7 - - + -
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASN 3.6 2.6 + - - -
106A VAL 3.1 1.4 + - - -
107A ILE* 1.3 81.3 - - + +
109A ILE* 1.3 58.1 + - - +
111A GLN* 4.2 5.8 - - - +
112A LYS* 2.9 30.2 + - - +
261A LEU* 5.0 0.6 - - - +
393A GLN* 3.1 6.0 + - - +
107D ILE* 5.5 0.9 - - + -
108D ALA* 3.5 23.8 - - + -
111D GLN* 3.7 5.8 + - - +
389D HIS* 3.6 3.8 - - - +
393D GLN* 2.8 35.1 - - - +
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Residues in contact with ILE 109 (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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106A VAL* 3.0 19.6 + - + +
108A ALA* 1.3 76.7 - - - +
110A LEU* 1.3 62.2 + - - +
112A LYS* 3.4 1.4 + - - +
113A ILE* 2.7 47.9 + - + +
143A PHE* 4.8 2.7 - - + -
147A PHE* 5.0 4.3 - - + -
256A PHE* 4.4 15.7 - - + -
261A LEU* 4.0 24.2 - - + -
268A TRP* 4.6 9.4 - - + -
389D HIS* 2.9 49.1 - - + -
392D ALA* 4.7 13.5 - - + -
393D GLN* 5.1 0.9 - - + +
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Residues in contact with LEU 110 (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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106A VAL 3.8 1.2 + - - -
107A ILE* 2.9 14.2 + - + +
109A ILE* 1.3 79.2 - - - +
111A GLN* 1.3 70.3 + - - +
113A ILE* 3.3 1.2 - - - +
114A SER* 2.9 29.1 + - - +
143A PHE* 3.3 33.0 - - + -
144A GLN* 4.6 7.2 - - + -
147A PHE* 3.5 34.3 - - + -
148A ASN* 5.0 3.8 - - - +
196A THR* 3.8 28.0 - - + +
312A ARG* 2.9 35.7 - - - +
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Residues in contact with GLN 111 (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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107A ILE* 2.9 38.4 + - + +
108A ALA* 4.1 2.4 - - - +
110A LEU* 1.3 78.2 - - + +
112A LYS* 1.3 67.3 + - - +
113A ILE 2.8 0.7 + - - -
114A SER 3.0 8.8 + - - -
115A ILE* 3.3 14.8 + - - +
196A THR* 4.0 22.7 - - + -
389A HIS* 2.6 35.5 + - + +
390A LEU* 4.6 5.3 - - + +
393A GLN* 3.3 15.6 - - - +
104D SER* 2.6 30.3 + - - +
105D ASN* 4.1 2.0 - - - +
107D ILE* 5.1 1.8 - - - +
108D ALA* 3.7 13.4 + - - +
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Residues in contact with LYS 112 (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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108A ALA 2.9 25.5 + - - +
109A ILE 3.6 5.2 - - - +
110A LEU 3.1 0.2 + - - -
111A GLN* 1.3 73.2 - - - +
113A ILE* 1.3 54.2 + - - +
115A ILE* 3.1 4.7 - - - +
116A ASN* 2.6 37.1 + - - +
259A CYS* 2.2 42.8 + - + +
260A GLN* 4.5 8.1 + - - +
261A LEU* 3.4 31.3 - - + +
393A GLN* 3.2 42.8 - - + +
395A ILE* 4.7 8.9 - - - +
112D LYS* 5.2 10.9 - - - +
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Residues in contact with ILE 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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109A ILE* 2.7 36.3 - - + +
110A LEU 3.3 7.6 - - - +
111A GLN 2.8 3.4 + - - -
112A LYS* 1.3 70.8 - - - +
114A SER* 1.3 57.3 + - - +
115A ILE 3.1 2.2 - - - -
116A ASN 2.9 1.6 + - - -
117A LEU* 2.5 43.0 + - + +
140A LEU* 4.8 2.2 - - + -
143A PHE* 2.8 42.2 - - + -
255A ILE* 4.3 15.7 - - + +
256A PHE* 4.4 13.7 - - + -
259A CYS* 3.0 36.6 - - + -
261A LEU* 4.3 5.2 - - + -
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Residues in contact with SER 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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110A LEU* 2.9 27.2 + - - +
111A GLN 3.7 2.5 - - - -
113A ILE* 1.3 80.9 - - - +
115A ILE* 1.3 61.5 + - - +
117A LEU* 3.0 2.8 + - - +
118A TRP* 2.9 29.5 + - - -
140A LEU* 3.5 15.9 - - - +
143A PHE* 4.7 0.2 - - - -
144A GLN* 3.1 26.0 + - - -
195A PHE* 3.8 10.8 - - - -
196A THR* 3.9 15.5 - - - +
390A LEU* 5.8 0.2 - - - -
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Residues in contact with ILE 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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111A GLN 3.3 8.2 + - - +
112A LYS 3.1 19.1 - - - +
114A SER* 1.3 80.0 - - - +
116A ASN* 1.3 74.0 + - - +
118A TRP* 2.9 26.0 + - - +
119A ASN* 3.0 13.6 + - - +
195A PHE* 5.3 3.3 - - + +
356A PHE* 4.2 11.1 - - + -
390A LEU* 2.6 51.3 - - + +
391A LEU* 3.2 21.1 - - + +
393A GLN* 4.3 4.5 - - + -
394A LEU* 3.4 25.6 - - + +
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Residues in contact with ASN 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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112A LYS* 2.6 28.4 + - - +
113A ILE 2.9 6.7 + - - +
115A ILE* 1.3 81.9 - - - +
117A LEU* 1.3 64.6 + - - +
118A TRP 3.4 0.2 - - - -
119A ASN* 4.0 11.3 + - - +
122A THR* 3.9 22.3 - - - +
136A LYS* 4.6 0.2 + - - -
255A ILE* 5.0 2.5 - - + +
258A TYR* 3.6 10.6 + - + -
259A CYS* 3.9 14.8 - - - -
393A GLN 3.1 21.0 + - - -
394A LEU* 3.0 21.5 - - - +
395A ILE* 2.8 33.5 + - - +
396A ASP 4.6 0.9 + - - -
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Residues in contact with LEU 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 ILE* 2.5 23.6 + - + +
114A SER 3.6 3.6 - - - +
116A ASN* 1.3 74.8 - - - +
118A TRP* 1.3 60.9 + - - +
119A ASN 3.5 0.2 - - - -
125A LEU* 5.9 2.7 - - + -
130A PHE* 5.3 9.6 - - + -
133A CYS* 5.8 0.2 - - - -
136A LYS* 3.3 53.4 - - + +
137A LEU* 4.4 6.8 - - - +
139A LEU* 4.1 17.7 - - + -
140A LEU* 3.5 45.5 - - + +
143A PHE* 6.4 0.2 - - + -
255A ILE* 3.8 34.1 - - + -
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Residues in contact with TRP 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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114A SER 2.9 30.1 + - - -
115A ILE* 2.9 7.7 + - - +
117A LEU* 1.3 78.0 - - - +
119A ASN* 1.3 65.5 + - - +
120A PRO* 2.9 9.9 - - - +
133A CYS* 4.6 1.4 - - - -
137A LEU* 3.7 28.5 - - + -
140A LEU* 3.5 11.9 - - + +
195A PHE* 2.7 44.8 + + + -
200A PHE* 3.9 26.5 - + - -
201A THR* 3.0 42.2 - - - -
204A VAL* 4.0 17.5 - - + -
352A LEU* 4.3 13.9 - - + -
356A PHE* 3.9 18.6 - - + -
359A HIS* 3.7 28.6 + - - -
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Residues in contact with ASN 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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115A ILE 3.0 11.9 + - - +
116A ASN* 4.0 9.9 + - - +
117A LEU 3.5 0.2 - - - -
118A TRP* 1.3 74.0 - - - +
120A PRO* 1.3 63.0 - - - +
121A SER* 2.6 39.6 + - - +
122A THR* 3.4 7.0 - - - +
136A LYS* 2.4 31.7 + - - +
258A TYR* 5.1 0.2 + - - -
356A PHE* 3.2 25.5 - - + -
394A LEU* 3.9 11.7 - - + +
396A ASP* 3.4 28.3 + - - +
398A THR* 3.9 4.4 - - - +
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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