Contacts of the helix formed by residues 102 - 113 (chain D) in PDB entry 5SY1
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 102 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100D PHE 3.6 2.5 + - - -
101D ILE* 1.3 78.7 - - - +
103D ALA* 1.3 59.8 + - - +
104D ALA* 3.1 10.7 + - - +
105D GLU* 2.6 45.4 + - - +
106D LEU* 2.9 25.3 + - - +
126D ILE* 5.5 2.9 - - - +
136D GLN* 3.8 15.0 + - - +
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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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102D SER* 1.3 73.7 - - - +
104D ALA* 1.3 59.0 + - - +
106D LEU* 3.4 9.2 + - - +
107D ARG* 3.1 54.1 + - - +
122D VAL* 5.3 4.3 - - + -
123D ASP* 5.1 7.9 - - - +
126D ILE* 4.8 18.6 - - + +
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Residues in contact with ALA 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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102D SER* 3.1 8.1 + - - +
103D ALA* 1.3 76.4 - - - +
105D GLU* 1.3 64.1 + - + +
106D LEU 3.2 0.2 - - - -
107D ARG* 3.4 20.8 + - - +
108D HIS* 3.4 19.1 + - - +
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Residues in contact with GLU 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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92D VAL 5.4 0.3 - - - +
93D PHE 3.8 16.3 - - - +
94D ASP* 3.0 11.3 - - - +
95D LYS* 4.2 14.9 + - + +
96D ASP* 2.2 39.9 + - - +
100D PHE 2.9 10.9 - - - +
101D ILE* 3.6 6.9 - - + -
102D SER* 2.6 28.5 + - - +
104D ALA* 1.3 72.3 - - + +
106D LEU* 1.3 63.6 + - - +
108D HIS* 3.6 16.4 - - - +
109D VAL* 3.8 10.4 - - - +
201D CA 2.4 18.6 - - - -
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Residues in contact with LEU 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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610B TRP* 4.7 7.6 - - + +
613B LEU* 4.4 21.1 - - + -
93D PHE* 4.9 16.8 - - + -
101D ILE* 4.6 10.1 - - + +
102D SER 2.9 18.2 + - - +
103D ALA* 3.6 6.1 - - - +
104D ALA 3.2 0.4 - - - -
105D GLU* 1.3 77.6 - - - +
107D ARG* 1.3 59.6 + - - +
109D VAL* 3.0 25.1 + - + +
110D MET* 3.4 14.5 + - + +
122D VAL* 3.7 27.8 - - + -
125D MET* 4.1 15.5 - - - -
126D ILE* 4.1 23.1 - - + -
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Residues in contact with ARG 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* 3.1 38.7 + - - +
104D ALA* 3.4 30.9 + - - +
105D GLU 3.5 0.4 - - - -
106D LEU* 1.3 74.0 - - - +
108D HIS* 1.3 54.2 - - - +
109D VAL 3.2 0.2 - - - -
110D MET* 3.8 14.8 - - - +
111D THR* 2.4 38.5 + - - +
115D GLU* 4.3 18.9 - - - +
119D ASP* 3.3 32.2 + - - +
122D VAL* 4.3 17.4 - - + +
123D ASP* 4.9 3.0 + - - -
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Residues in contact with HIS 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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92D VAL* 5.2 6.7 - - + -
95D LYS* 3.2 43.4 + - + -
104D ALA 3.4 11.5 + - - +
105D GLU* 3.6 14.6 - - - +
106D LEU 3.1 0.6 - - - -
107D ARG* 1.3 79.3 - - - +
109D VAL* 1.3 61.2 + - + +
111D THR* 3.4 10.6 - - + +
112D ASN* 2.9 54.1 + - - -
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Residues in contact with VAL 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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613B LEU* 5.1 9.4 - - + -
617B VAL* 4.3 10.5 - - + -
92D VAL* 4.1 25.1 - - + +
93D PHE* 4.1 34.8 - - + -
105D GLU 3.8 11.7 - - - +
106D LEU* 3.0 12.7 + - + +
108D HIS* 1.3 80.6 - - + +
110D MET* 1.3 59.5 + - + +
112D ASN* 3.1 12.8 + - + +
113D LEU* 2.9 43.1 + - + +
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Residues in contact with MET 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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613B LEU* 4.7 22.9 - - + -
106D LEU* 3.4 14.2 + - + +
107D ARG* 3.6 13.9 + - - +
109D VAL* 1.3 73.9 - - - +
111D THR* 1.3 57.6 + - - +
113D LEU* 4.1 5.6 - - - +
114D GLY 2.7 14.9 + - - -
115D GLU* 2.4 43.3 + - + +
116D LYS* 3.6 11.9 - - + +
117D LEU* 3.6 48.5 - - + +
122D VAL* 3.9 25.1 - - + -
125D MET* 5.0 7.0 - - + -
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Residues in contact with THR 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 ARG* 2.4 28.8 + - - +
108D HIS* 3.4 14.0 - - + +
109D VAL 3.2 0.2 - - - -
110D MET* 1.3 77.8 - - - +
112D ASN* 1.3 63.4 + - - +
114D GLY* 4.0 4.7 + - - -
115D GLU* 4.1 17.4 + - - +
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Residues in contact with ASN 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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623B VAL* 5.3 0.3 - - - +
627B LYS* 4.2 5.0 + - - -
92D VAL* 5.8 5.1 - - - +
108D HIS* 2.9 47.6 + - - -
109D VAL* 3.1 13.7 + - + +
111D THR* 1.3 78.6 - - - +
113D LEU* 1.3 71.7 + - + +
114D GLY 3.6 0.6 + - - -
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Residues in contact with LEU 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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613B LEU* 4.7 14.1 - - + -
616B LEU* 4.1 31.7 - - + +
617B VAL* 4.5 11.9 - - + -
623B VAL* 3.7 32.3 - - + -
626B ARG* 5.0 7.3 + - - -
627B LYS* 3.2 17.0 - - - +
109D VAL* 2.9 32.9 + - + +
110D MET* 3.1 8.1 + - - -
112D ASN* 1.3 92.3 - - + +
114D GLY* 1.3 54.9 + - - +
115D GLU 3.5 2.3 + - - -
116D LYS* 5.1 3.3 + - - +
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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