Contacts of the helix formed by residues 101 - 111 (chain D) in PDB entry 4IA4
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 ASN 101 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85D ILE* 6.2 1.8 - - + +
99D HIS 2.7 6.0 + - - +
100D ILE* 1.3 81.4 - - - +
102D PRO* 1.3 64.4 - - - +
103D ALA* 2.8 22.6 + - - +
104D VAL* 2.7 45.3 + - + +
105D THR* 2.9 12.1 + - - -
126D GLN* 2.9 7.8 + - - -
175D LEU* 3.9 13.5 - - - +
221D ILE 2.7 25.2 + - - -
222D ASN* 2.8 24.3 - - - +
223D PRO* 3.5 4.3 - - - +
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Residues in contact with PRO 102 (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 ASN* 1.3 87.6 - - - +
103D ALA* 1.3 50.9 + - - +
105D THR* 3.0 4.9 + - - +
106D PHE* 2.6 38.7 + - - +
123D MET* 3.9 28.3 - - + +
126D GLN* 2.6 17.4 - - + +
127D CYS* 6.2 0.7 - - - -
222D ASN* 3.5 4.9 - - - +
223D PRO* 3.9 15.7 - - + -
224D ALA* 3.4 40.4 - - + +
246D TRP* 5.3 5.6 - - + -
250D PHE* 4.2 8.5 - - + -
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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
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101D ASN* 2.8 17.4 + - - +
102D PRO* 1.3 75.5 - - - +
104D VAL* 1.3 59.0 + - + +
106D PHE* 4.0 7.9 - - - -
107D GLY* 3.0 22.5 + - - -
172D THR* 4.1 12.1 - - + -
176D VAL* 4.1 2.0 - - + +
221D ILE* 4.3 1.1 - - + +
223D PRO* 4.0 4.1 - - + +
249D PRO* 3.7 41.1 - - + +
250D PHE* 5.1 2.2 - - - -
253D ALA* 3.2 12.8 - - - +
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Residues in contact with VAL 104 (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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99D HIS* 4.1 29.2 - - + +
101D ASN* 2.7 34.7 + - + +
103D ALA* 1.3 72.7 - - + +
105D THR* 1.3 66.4 + - - +
107D GLY* 3.8 0.3 + - - -
108D LEU* 3.3 25.9 + - + +
175D LEU* 4.4 16.8 - - + -
176D VAL* 4.7 8.6 - - + +
179D VAL* 4.1 38.5 - - + +
197D LEU* 4.9 4.3 - - + -
202D ILE* 6.3 0.4 - - + -
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Residues in contact with THR 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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99D HIS* 3.1 30.0 + - + +
101D ASN 2.9 11.5 + - - -
102D PRO* 3.4 6.5 - - - -
104D VAL* 1.3 75.5 - - - +
106D PHE* 1.3 55.1 + - - +
108D LEU* 2.9 5.0 + - - +
109D PHE* 2.7 35.0 + - - +
114D VAL* 4.7 6.0 - - + +
119D ALA* 3.9 31.6 - - + +
122D TYR* 3.9 14.8 - - + -
123D MET* 4.3 6.1 - - + -
126D GLN* 3.2 17.8 + - - -
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Residues in contact with PHE 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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102D PRO 2.6 20.0 + - - +
103D ALA* 3.8 3.8 - - - +
105D THR* 1.3 72.6 - - - +
107D GLY* 1.3 57.4 + - - +
109D PHE* 3.1 18.6 + + - +
110D LEU* 3.0 71.2 + - + +
123D MET* 3.7 13.8 - - + +
250D PHE* 3.2 69.1 - + + -
253D ALA* 4.0 6.7 - - + -
254D ALA* 4.2 4.0 - - + -
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Residues in contact with GLY 107 (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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103D ALA 3.0 17.5 + - - -
104D VAL 4.3 0.7 - - - -
106D PHE* 1.3 77.1 - - - +
108D LEU* 1.3 62.1 + - - +
110D LEU* 3.3 10.4 + - - +
111D ALA* 3.3 15.6 + - - +
176D VAL* 5.0 2.9 - - - -
180D PHE* 3.4 18.4 - - - -
253D ALA* 4.0 22.9 - - - -
257D ALA* 3.8 2.5 - - - +
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Residues in contact with LEU 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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99D HIS* 3.3 33.2 - - + +
104D VAL* 3.3 24.2 + - + +
105D THR 2.9 4.8 + - - +
107D GLY* 1.3 76.8 - - - +
109D PHE* 1.3 60.4 + - - +
111D ALA* 3.3 3.9 + - - +
112D ARG 3.2 3.3 + - - -
113D LYS* 3.0 42.7 + - + +
114D VAL* 3.8 16.3 + - + -
179D VAL* 4.5 11.7 - - + -
180D PHE* 3.3 31.9 - - + -
183D THR* 4.7 11.0 - - + -
194D VAL* 5.4 3.4 - - + -
195D PRO* 5.5 4.5 - - + +
197D LEU* 5.1 7.4 - - + -
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Residues in contact with PHE 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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105D THR 2.7 12.2 + - - +
106D PHE* 3.2 24.7 - + - +
107D GLY 3.1 0.2 - - - -
108D LEU* 1.3 74.2 - - - +
110D LEU* 1.3 78.3 + - + +
111D ALA 2.9 5.2 - - - -
112D ARG* 2.8 23.9 + - + +
114D VAL* 3.5 24.6 - - + +
115D SER 4.6 0.7 - - - -
116D LEU* 3.9 46.7 - - + -
119D ALA* 4.4 16.8 - - + -
123D MET* 5.6 1.8 - - + -
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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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106D PHE* 3.0 62.3 + - + +
107D GLY* 3.3 8.2 + - - +
109D PHE* 1.3 90.2 - - + +
111D ALA* 1.3 55.7 + - - +
112D ARG* 3.2 3.1 + - - +
253D ALA 4.9 0.4 - - - +
254D ALA* 3.8 25.6 - - + +
257D ALA* 4.6 8.5 - - + -
261D GLN* 4.8 0.5 - - - +
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Residues in contact with ALA 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 GLY 3.3 10.7 + - - +
108D LEU 3.4 10.8 - - - +
109D PHE 2.9 0.6 - - - -
110D LEU* 1.3 77.1 - - - +
112D ARG* 1.3 69.9 + - - +
113D LYS* 3.5 11.9 + - + +
180D PHE* 3.9 16.8 - - + -
257D ALA* 5.1 2.5 - - + -
261D GLN* 3.4 40.7 - - - +
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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