Contacts of the helix formed by residues 105 - 117 (chain D) in PDB entry 5SWW
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 105 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B HIS* 6.6 0.2 - - - -
185B ALA* 5.1 3.5 - - - +
73D LEU* 5.5 2.5 - - - -
102D PHE 3.1 12.4 + - - -
103D SER 3.4 1.2 + - - -
104D TRP* 1.3 77.6 - - - +
106D CYS* 1.3 59.8 + - - +
107D ALA 3.5 1.8 - - - -
108D GLY* 3.5 5.5 + - - -
109D GLU* 2.9 36.4 + - - +
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Residues in contact with CYS 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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70D HIS* 3.6 17.3 - - - -
72D ALA* 4.0 22.4 - - + -
73D LEU* 4.2 17.0 - - - -
100D PRO* 4.5 2.9 - - + -
101D CYS* 3.5 15.9 + - - +
104D TRP 3.4 2.4 - - - -
105D GLY* 1.3 76.6 - - - +
107D ALA* 1.3 59.0 - - - +
109D GLU* 3.2 4.1 + - - +
110D VAL* 2.8 36.7 + - - +
201D ZN 2.3 37.0 - - - -
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Residues in contact with ALA 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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100D PRO* 5.0 0.6 - - - +
101D CYS 2.9 20.4 + - - +
102D PHE* 4.2 6.9 - - + +
105D GLY 3.5 0.2 - - - -
106D CYS* 1.3 75.1 - - - +
108D GLY* 1.3 58.4 + - - +
110D VAL* 4.0 1.7 - - - +
111D ARG* 3.0 28.2 + - - +
139D ALA* 3.8 32.3 - - + +
142D MET* 3.6 17.7 - - + +
143D LEU* 4.1 17.5 - - + +
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Residues in contact with GLY 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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181B GLU* 3.8 21.5 - - - -
102D PHE* 5.5 2.2 + - - -
105D GLY* 3.5 8.8 + - - -
106D CYS 3.2 0.6 - - - -
107D ALA* 1.3 80.1 - - - +
109D GLU* 1.3 56.6 + - - +
111D ARG* 3.3 8.1 + - - +
112D ALA* 2.9 27.4 + - - +
142D MET* 3.6 17.2 - - - -
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Residues in contact with GLU 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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73D LEU* 3.6 30.5 - - + -
76D LEU* 3.9 10.2 - - + +
105D GLY* 2.9 21.5 + - - +
106D CYS 3.8 1.1 - - - +
108D GLY* 1.3 74.0 - - - +
110D VAL* 1.3 62.5 + - - +
112D ALA* 3.2 11.7 + - + +
113D PHE* 2.9 27.9 + - - +
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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
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72D ALA* 4.3 11.9 - - + -
73D LEU* 6.1 0.2 - - + -
76D LEU* 4.3 16.4 - - + -
94D TRP* 4.1 23.1 - - + -
100D PRO* 5.5 2.0 - - + -
106D CYS* 2.8 23.0 + - - +
109D GLU* 1.3 75.5 - - - +
111D ARG* 1.3 58.9 + - - +
113D PHE* 3.2 6.7 + - + +
114D LEU* 2.9 35.0 + - + +
122D LEU* 3.7 29.8 - - + -
124D ILE* 5.0 0.4 - - + -
143D LEU* 3.7 25.8 - - + -
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Residues in contact with ARG 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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178B GLY* 5.8 3.0 - - - -
181B GLU* 2.6 36.3 + - - +
107D ALA 3.0 19.3 + - - +
108D GLY 3.6 7.7 + - - +
110D VAL* 1.3 77.6 - - - +
112D ALA* 1.3 58.4 + - - +
114D LEU* 3.2 2.6 + - - +
115D GLN* 2.9 61.7 + - - +
142D MET* 4.1 26.9 - - + +
143D LEU* 5.1 0.4 - - + +
145D ASP 6.2 0.4 - - - -
146D ALA* 3.6 33.0 - - + +
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Residues in contact with ALA 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 GLY 2.9 15.1 + - - +
109D GLU* 3.2 19.0 + - + +
111D ARG* 1.3 82.3 - - - +
113D PHE* 1.3 56.6 + - - +
115D GLN* 3.1 10.9 + - - +
116D GLU* 2.9 43.7 + - + +
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Residues in contact with PHE 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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75D PHE* 5.4 4.9 - + - -
76D LEU* 3.6 33.2 - - + -
79D VAL* 3.6 43.3 - - + -
84D LEU* 5.4 0.2 - - + -
109D GLU 2.9 13.9 + - - +
110D VAL* 3.2 8.5 + - + +
112D ALA* 1.3 75.1 - - - +
114D LEU* 1.3 70.5 + - + +
116D GLU* 4.8 2.2 - - - -
117D ASN* 2.9 56.5 + - - +
120D VAL* 3.7 40.4 - - + -
122D LEU* 6.2 2.0 - - + -
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Residues in contact with LEU 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* 2.9 30.2 + - + +
111D ARG* 3.2 5.1 + - - +
113D PHE* 1.3 92.1 - - + +
115D GLN* 1.3 60.9 + - + +
117D ASN 3.3 17.0 - - - +
118D THR* 4.0 6.8 + - - +
120D VAL* 3.9 20.4 - - + +
121D ARG* 5.1 0.2 - - - -
122D LEU* 3.9 25.1 - - + +
143D LEU* 5.9 0.4 - - + -
146D ALA* 3.6 38.8 - - + +
147D GLY 4.9 0.4 - - - -
148D ALA* 3.8 24.5 - - + +
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Residues in contact with GLN 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 ARG* 2.9 56.1 + - + +
112D ALA* 3.1 8.9 + - - +
114D LEU* 1.3 79.2 - - + +
116D GLU* 1.3 72.6 + - - +
118D THR* 3.6 14.0 + - - -
146D ALA* 5.9 2.4 - - + +
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Residues in contact with GLU 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 ALA* 2.9 28.9 + - + +
113D PHE* 4.8 1.6 - - - -
115D GLN* 1.3 84.8 - - - +
117D ASN* 1.3 69.8 + - - +
118D THR* 3.6 5.2 + - - -
119D HIS* 5.4 0.3 - - - -
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Residues in contact with ASN 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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79D VAL* 5.4 2.6 - - - +
113D PHE* 2.9 53.4 + - + +
114D LEU* 3.3 12.2 - - - +
116D GLU* 1.3 85.9 + - - +
118D THR* 1.3 64.1 + - - +
119D HIS* 3.1 38.3 + - + +
120D VAL* 3.4 16.4 + - + +
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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