Contacts of the helix formed by residues 123 - 136 (chain P) in PDB entry 5D4D
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 ASP 123 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117P SER* 4.4 0.2 - - - -
122P LEU* 1.3 74.8 - - - +
124P PRO* 1.3 78.7 - - - +
125P ASP* 3.3 27.7 - - - +
126P LEU* 3.6 18.8 + - + +
127P ILE* 3.1 23.3 + - - +
146P GLY 5.2 0.7 - - - +
147P LEU* 4.2 6.8 - - - +
148P LYS* 5.3 13.4 + - + +
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Residues in contact with PRO 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113P ILE* 3.7 18.3 - - + +
114P LYS* 4.1 27.8 - - + +
117P SER* 3.2 32.3 - - - +
122P LEU 3.6 1.1 - - - +
123P ASP* 1.3 95.1 - - - +
125P ASP* 1.3 63.1 + - - +
127P ILE* 3.5 2.3 + - + +
128P ARG* 2.9 33.3 + - - +
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Residues in contact with ASP 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123P ASP* 3.2 22.7 - - - +
124P PRO* 1.3 82.8 - - - +
126P LEU* 1.3 55.5 + - - +
128P ARG* 3.3 32.9 + - - +
129P GLU* 2.9 34.0 + - + +
146P GLY 4.1 13.5 - - - +
147P LEU* 3.9 13.5 - - + -
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Residues in contact with LEU 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122P LEU* 4.2 18.6 - - + -
123P ASP* 3.2 21.6 + - + +
125P ASP* 1.3 79.1 - - - +
127P ILE* 1.3 58.6 + - - +
129P GLU* 3.2 3.9 + - - +
130P VAL* 2.9 40.3 + - + +
147P LEU* 3.6 15.0 - - + +
149P GLU* 3.7 31.0 - - - +
151P LEU* 4.1 22.0 - - + -
155P THR* 4.6 3.8 - - + -
159P ILE* 4.0 30.7 - - + -
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Residues in contact with ILE 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113P ILE* 4.5 13.0 - - + +
116P LEU* 3.6 53.6 - - + +
117P SER* 3.8 8.1 - - - +
120P THR* 4.4 1.3 - - - +
122P LEU* 4.0 29.8 - - + -
123P ASP 3.1 12.4 + - - +
124P PRO 3.9 4.3 - - - +
126P LEU* 1.3 75.4 - - - +
128P ARG* 1.3 64.5 + - - +
130P VAL* 3.2 6.4 + - - +
131P VAL* 2.9 42.2 + - + +
159P ILE* 5.0 3.8 - - + -
163P LEU* 4.4 17.9 - - + -
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Residues in contact with ARG 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110P MET* 6.5 1.1 - - - -
113P ILE* 3.7 25.3 - - + +
124P PRO* 2.9 20.5 + - - +
125P ASP* 3.3 50.2 + - - +
127P ILE* 1.3 77.8 - - - +
129P GLU* 1.3 80.1 + - - +
131P VAL* 3.7 2.2 - - - +
132P ARG* 2.9 48.4 + - - +
144P ILE* 6.0 2.0 - - - +
146P GLY 5.8 0.4 + - - -
181P GLU* 3.6 19.1 - - - +
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Residues in contact with GLU 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559N ALA 4.5 1.0 - - - +
125P ASP 2.9 21.4 + - - +
126P LEU 3.7 4.5 - - - +
128P ARG* 1.3 105.3 + - - +
130P VAL* 1.3 57.2 + - - +
132P ARG* 3.2 37.7 + - - +
133P ALA* 2.9 27.5 + - - +
142P ARG* 5.2 4.9 + - - -
144P ILE* 3.6 36.1 - - + +
147P LEU* 4.4 18.4 - - + -
151P LEU* 4.3 14.7 - - + +
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Residues in contact with VAL 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126P LEU* 2.9 31.6 + - + +
127P ILE* 3.2 4.0 + - - +
129P GLU* 1.3 74.9 - - - +
131P VAL* 1.3 61.3 + - - +
133P ALA* 3.2 7.1 + - - +
134P LYS* 2.9 29.4 + - + +
151P LEU* 4.6 4.0 - - + -
155P THR 4.7 0.2 - - - +
156P VAL* 3.7 39.7 - - + +
159P ILE* 3.8 34.8 - - + -
160P ASP* 4.0 13.9 - - + +
163P LEU* 4.8 5.2 - - + -
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Residues in contact with VAL 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113P ILE* 5.1 1.6 - - + -
116P LEU* 5.4 0.7 - - + -
127P ILE* 2.9 35.4 + - + +
128P ARG* 3.7 5.4 - - - +
130P VAL* 1.3 75.8 - - - +
132P ARG* 1.3 59.2 + - - +
134P LYS* 3.1 4.7 + - - +
135P ILE* 2.9 27.5 + - - +
160P ASP* 6.1 0.2 - - - -
163P LEU* 4.6 12.6 - - + -
174P LEU* 4.6 9.2 - - + -
177P ALA* 3.7 17.0 - - + +
178P ARG* 3.6 39.3 - - - +
181P GLU* 3.6 20.4 - - + -
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Residues in contact with ARG 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559N ALA 3.2 21.0 + - - -
560N GLN* 3.4 18.1 + - - +
561N GLY* 3.5 15.0 - - - +
128P ARG* 2.9 44.5 + - - +
129P GLU* 3.2 32.7 + - - +
131P VAL* 1.3 73.9 - - - +
133P ALA* 1.3 61.4 + - - +
135P ILE* 3.8 2.9 - - - +
136P LEU* 2.9 47.9 + - + +
142P ARG* 4.8 6.5 - - - +
144P ILE* 5.3 0.2 - - - +
181P GLU* 3.7 22.5 + - + +
184P ARG* 3.7 29.0 - - - +
185P GLN* 4.9 2.0 - - - +
225P GLU* 4.9 5.7 + - - -
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Residues in contact with ALA 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P GLU 2.9 20.3 + - - +
130P VAL* 3.2 10.7 + - - +
132P ARG* 1.3 77.7 - - - +
134P LYS* 1.3 58.8 + - - +
136P LEU* 3.8 0.8 - - - +
137P GLY* 2.9 33.1 + - - +
140P ARG 5.0 2.0 - - - -
141P VAL* 4.8 11.1 - - + +
142P ARG* 4.7 13.9 - - - +
151P LEU* 4.6 5.4 - - + -
156P VAL* 4.2 23.3 - - + -
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Residues in contact with LYS 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412N GLY 3.3 23.5 - - - +
413N ASP* 4.8 8.0 - - - +
130P VAL* 2.9 18.5 + - + +
131P VAL* 3.1 1.1 + - - +
133P ALA* 1.3 76.8 - - + +
135P ILE* 1.3 65.4 - - - +
137P GLY* 3.6 9.9 + - - +
156P VAL* 4.2 22.1 - - + +
157P GLU* 3.8 19.0 + - - -
160P ASP* 3.6 35.7 - - + +
178P ARG* 3.5 26.2 - - - +
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Residues in contact with ILE 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163N TYR* 6.0 0.7 - - - -
411N THR* 3.4 28.7 - - + +
412N GLY* 4.0 8.7 - - - -
434N ARG* 3.2 28.4 + - - +
131P VAL 2.9 18.3 + - - +
132P ARG* 3.2 4.5 + - + +
134P LYS* 1.3 75.9 - - - +
136P LEU* 1.3 65.7 + - + +
137P GLY* 3.0 5.3 + - - -
178P ARG* 3.4 32.8 - - - +
181P GLU* 3.8 15.0 - - + -
182P ALA* 4.0 29.2 - - + +
185P GLN* 4.5 12.3 - - + -
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Residues in contact with LEU 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162N ARG* 4.9 3.8 + - - -
163N TYR* 5.2 5.8 + - - -
561N GLY* 4.6 3.6 - - - -
563N PRO* 5.9 0.2 - - + -
564N GLU 6.2 0.7 - - - +
132P ARG* 2.9 39.3 + - + +
133P ALA 4.2 2.9 - - - +
135P ILE* 1.3 77.5 - - + +
137P GLY* 1.3 65.4 + - - +
138P SER 4.3 0.5 - - - -
139P ALA* 3.8 16.8 + - + +
140P ARG* 3.9 44.9 - - + +
142P ARG* 4.2 17.0 - - - +
185P GLN* 3.7 34.5 - - + +
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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