Contacts of the helix formed by residues 115 - 124 (chain D) in PDB entry 4WYV
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 THR 115 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D LEU 3.3 4.2 + - - -
114D VAL* 1.3 77.1 - - - +
116D ARG* 1.3 64.5 + - - +
117D GLU* 2.6 26.4 + - + +
118D ALA* 3.2 29.6 + - + +
119D VAL* 3.1 19.2 + - - +
140D TYR* 3.8 3.1 - - - -
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Residues in contact with ARG 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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115D THR* 1.3 74.3 + - - +
117D GLU* 1.3 81.3 + - - +
119D VAL* 3.1 6.6 + - - +
120D THR* 3.0 26.8 + - + +
128D ASP* 3.2 38.3 + - - +
135D LEU* 3.0 35.2 + - + +
136D ASP 4.5 1.8 - - - -
137D VAL* 4.1 24.9 - - - +
140D TYR* 3.6 55.3 + - + -
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Residues in contact with GLU 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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115D THR* 2.6 32.1 + - + +
116D ARG* 1.3 97.1 + - - +
118D ALA* 1.3 56.9 + - - +
120D THR* 2.3 34.6 + - - +
121D GLU* 3.0 20.9 + - - +
127D PRO* 5.0 15.0 - - + -
129D ARG* 5.1 11.7 - - - +
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Residues in contact with ALA 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 VAL* 3.6 12.8 - - + -
115D THR* 3.2 30.0 + - + +
117D GLU* 1.3 79.1 - - - +
119D VAL* 1.3 60.5 + - - +
121D GLU* 3.1 16.1 + - - +
122D ILE* 3.0 32.9 + - + +
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Residues in contact with VAL 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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99D VAL* 4.1 22.9 - - + -
102D ALA* 4.2 11.4 - - + -
114D VAL* 3.5 26.5 - - + -
115D THR 3.1 16.2 + - - +
116D ARG 3.1 7.8 + - - +
118D ALA* 1.3 70.6 - - - +
120D THR* 1.3 68.5 + - - +
122D ILE* 3.1 10.5 + - - +
123D LEU* 3.0 37.7 + - + +
135D LEU* 3.9 17.5 - - + -
140D TYR* 4.1 13.7 - - + -
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Residues in contact with THR 120 (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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116D ARG* 3.0 20.9 - - + +
117D GLU* 2.3 31.3 + - - +
119D VAL* 1.3 77.5 - - - +
121D GLU* 1.3 63.8 + - - +
123D LEU* 3.2 1.7 + - - -
124D GLY 3.2 3.3 + - - -
125D ILE* 2.8 51.3 + - - +
126D GLU 3.9 18.6 - - - +
127D PRO* 4.4 13.4 - - + +
135D LEU* 3.9 23.8 - - + -
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Residues in contact with GLU 121 (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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69D LYS* 3.8 11.1 - - - -
117D GLU* 3.0 19.0 + - - +
118D ALA* 3.4 15.9 - - - +
119D VAL 3.1 0.4 - - - -
120D THR* 1.3 81.8 + - - +
122D ILE* 1.3 66.0 + - + +
124D GLY* 3.3 10.7 + - - -
125D ILE 4.6 2.2 - - - +
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Residues in contact with ILE 122 (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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62D ARG* 3.8 27.8 - - + +
65D PHE* 3.6 46.1 - - + +
69D LYS* 3.0 26.6 + - - +
102D ALA* 4.3 14.8 - - + +
106D VAL* 4.5 11.7 - - + -
114D VAL* 4.3 13.9 - - + -
118D ALA* 3.0 28.9 + - + +
119D VAL* 3.1 11.0 + - - +
121D GLU* 1.3 76.9 - - + +
123D LEU* 1.3 58.6 + - + +
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Residues in contact with LEU 123 (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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65D PHE* 3.9 18.4 - - + -
68D VAL* 3.8 22.4 - - + -
69D LYS* 3.6 15.3 - - - -
72D LEU* 3.1 22.6 - - + +
95D LEU* 4.0 26.9 - - + -
98D LEU* 3.7 30.3 - - + +
99D VAL* 5.0 1.8 - - + +
102D ALA* 5.5 0.4 - - + -
119D VAL* 3.0 36.5 + - + +
120D THR* 3.8 2.5 - - - +
121D GLU 3.2 0.4 - - - -
122D ILE* 1.3 78.9 - - + +
124D GLY* 1.3 58.2 + - - +
125D ILE* 3.8 18.3 - - + +
135D LEU* 5.2 3.6 - - + -
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Residues in contact with GLY 124 (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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69D LYS* 3.7 21.5 - - - +
72D LEU* 5.2 0.7 - - - +
73D THR* 5.3 2.8 + - - -
76D LYS* 3.3 21.7 + - - -
120D THR 3.2 2.9 + - - -
121D GLU* 3.3 10.8 + - - -
122D ILE 3.3 1.2 + - - -
123D LEU* 1.3 78.3 - - - +
125D ILE* 1.3 61.9 + - - +
126D GLU* 4.1 2.0 - - - +
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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