Contacts of the helix formed by residues 118 - 133 (chain A) in PDB entry 4L0D
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 VAL 118 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLU* 3.5 33.0 - - + +
113A ASN* 4.0 0.2 - - - +
117A SER* 1.3 74.1 - - - +
119A LYS* 1.3 87.1 + - + +
121A ARG* 3.0 23.4 + - - +
122A ILE 4.0 0.5 + - - -
232A HIS* 3.3 32.1 + - + +
236A THR* 6.4 0.2 - - + -
260A THR* 4.1 8.3 - - + +
373A ILE* 5.5 5.2 - - + -
375A PRO* 2.9 33.1 + - + +
601A PLP 4.5 8.1 - - + +
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Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER* 3.1 7.8 - - - +
118A VAL* 1.3 82.3 - - + +
120A ASP* 1.3 67.4 + - - +
122A ILE* 3.0 19.5 + - + +
123A SER* 2.9 25.9 + - - -
146A THR* 5.7 0.4 - - - -
147A SER* 6.0 1.8 - - - -
149A ASN* 3.4 20.2 - - + -
150A THR* 2.9 42.6 - - - +
222A GLN* 4.1 7.9 - - - -
232A HIS* 6.3 1.6 - - + -
257A THR* 4.9 4.0 - - - -
601A PLP 1.4 88.1 + - - +
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Residues in contact with ASP 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 3.8 22.2 - - + +
113A ASN* 3.3 13.5 - - + +
115A GLY* 2.5 43.7 + - - -
116A GLY 2.9 8.9 + - - -
117A SER* 3.3 24.1 + - - +
118A VAL 3.1 0.6 + - - -
119A LYS* 1.3 77.2 - - - +
121A ARG* 1.3 64.5 + - - +
123A SER* 3.7 7.1 - - - -
124A LEU* 3.3 19.6 + - - +
149A ASN 4.4 0.2 - - - +
152A ILE* 4.6 0.5 - - - +
153A GLY* 3.6 19.3 + - - -
156A LEU* 5.3 1.3 - - + -
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Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 3.8 19.7 - - + +
85A GLY* 4.0 13.6 - - - +
87A THR* 3.2 8.7 + - - -
108A LYS* 4.1 3.8 - - - +
110A GLU* 2.3 36.2 + - - +
113A ASN* 4.5 4.0 - - - +
118A VAL* 3.0 15.7 + - - +
120A ASP* 1.3 77.9 - - - +
122A ILE* 1.3 71.1 + - + +
124A LEU* 2.9 16.3 + - - +
125A ARG* 3.1 13.5 + - - +
231A ALA* 4.8 8.1 - - + -
232A HIS* 4.4 9.9 - - - -
235A THR* 2.7 35.0 + - - +
236A THR* 3.2 23.4 + - - +
239A GLU* 3.0 40.4 + - - -
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL 4.9 0.2 - - - +
119A LYS* 3.0 26.1 + - + +
121A ARG* 1.3 72.8 - - + +
123A SER* 1.3 66.1 + - - +
125A ARG* 4.4 0.2 - - - -
126A MET* 3.0 49.8 + - - +
150A THR* 3.6 30.1 - - + +
222A GLN* 4.2 11.9 - - + +
228A ASN* 3.1 44.4 - - + +
231A ALA* 4.2 10.8 - - + -
232A HIS* 3.3 27.8 - - + +
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LYS 2.9 17.2 + - - -
120A ASP 3.7 4.9 - - - -
121A ARG 3.0 0.2 + - - -
122A ILE* 1.3 79.0 - - - +
124A LEU* 1.3 68.7 + - - +
126A MET* 3.0 13.7 + - - +
127A ILE* 3.0 18.9 + - - +
150A THR* 3.3 25.8 + - - +
153A GLY* 3.4 26.6 - - - -
154A LEU* 3.4 17.9 + - - +
157A ALA* 5.6 0.9 - - - -
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LEU* 3.7 43.5 - - + +
82A LYS* 5.5 6.3 - - + +
84A ILE* 4.0 15.7 - - + +
120A ASP 3.3 9.5 + - - +
121A ARG* 2.9 8.8 + - - +
123A SER* 1.3 78.7 - - - +
125A ARG* 1.3 64.9 + - - +
127A ILE* 2.9 12.0 + - + +
128A GLU* 2.9 50.7 + - + +
157A ALA* 5.1 7.2 - - + -
161A ARG* 4.1 17.7 - - - +
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Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A HIS* 3.1 24.9 + - - -
68A THR* 3.7 22.5 + - - +
121A ARG 3.1 8.2 + - - +
122A ILE 4.0 1.8 - - - +
124A LEU* 1.3 79.3 - - - +
126A MET* 1.3 63.8 + - - +
128A GLU* 2.9 13.8 + - - +
129A ASP* 2.9 53.2 + - - +
132A ARG* 5.2 2.7 - - - +
227A SER* 3.3 21.5 - - - +
230A LEU* 4.0 18.2 - - - +
231A ALA* 3.5 36.9 - - + +
234A ASP* 2.9 33.7 + - - +
235A THR* 5.1 4.2 - - - +
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Residues in contact with MET 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 3.0 48.4 + - - +
123A SER* 3.0 6.9 + - - +
125A ARG* 1.3 75.6 - - - +
127A ILE* 1.3 62.8 + - - +
129A ASP* 4.0 1.7 - - - +
130A ALA* 3.0 23.6 + - - +
144A GLU* 4.8 2.9 - - - +
150A THR* 5.3 2.0 - - - -
154A LEU* 5.9 2.5 - - + -
220A LEU* 3.4 51.0 - - + +
221A ASP 4.0 0.2 - - - +
222A GLN* 3.4 34.5 - - + +
225A ASN* 3.7 12.2 + - + +
227A SER* 3.6 25.4 + - - -
228A ASN* 4.2 8.7 - - - +
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A SER 3.0 11.2 + - - +
124A LEU* 2.9 9.9 + - + +
126A MET* 1.3 75.2 - - - +
128A GLU* 1.3 60.5 + - + +
130A ALA* 2.9 6.8 + - - +
131A GLU* 2.8 45.5 + - - +
136A LEU* 3.7 17.0 - - + -
142A ILE* 4.0 13.5 - - + -
154A LEU* 3.5 29.8 - - + +
157A ALA* 3.8 28.0 - - + -
158A ALA 5.2 0.2 - - - +
161A ARG* 4.6 7.2 - - - +
163A TYR* 3.8 12.6 - - + -
220A LEU* 3.7 11.4 - - + -
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Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A LYS* 4.4 9.2 + - - -
124A LEU* 2.9 38.8 + - + +
125A ARG* 3.7 13.6 - - - +
127A ILE* 1.3 75.7 - - + +
129A ASP* 1.3 63.5 + - - +
131A GLU* 2.9 29.7 + - - +
132A ARG* 3.0 43.5 + - - +
161A ARG* 3.5 23.6 + - - +
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Residues in contact with ASP 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A HIS* 4.1 15.2 - - - +
125A ARG* 2.9 42.7 + - - +
126A MET 4.0 1.1 - - - +
128A GLU* 1.3 74.6 - - - +
130A ALA* 1.3 64.9 + - - +
132A ARG* 2.9 35.5 + - - +
133A ASP* 3.1 22.7 + - - +
227A SER* 2.9 33.7 + - - +
230A LEU* 5.4 2.3 - - - +
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A MET 3.0 19.6 + - - +
127A ILE 2.9 8.8 + - - +
129A ASP* 1.3 76.8 - - - +
131A GLU* 1.3 58.3 + - - +
133A ASP* 4.4 3.8 - - - -
134A GLY 3.7 0.5 + - - -
135A THR* 2.6 32.3 + - - +
136A LEU* 3.0 29.7 + - + -
220A LEU* 4.1 19.3 - - + -
225A ASN* 6.1 0.7 - - - +
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ILE* 2.8 25.1 + - + +
128A GLU* 2.9 17.0 + - - +
130A ALA* 1.3 79.1 - - - +
132A ARG* 1.3 65.3 + - + +
134A GLY* 3.2 12.5 + - - -
136A LEU* 4.1 14.1 - - + +
161A ARG* 2.7 38.3 + - - -
163A TYR* 3.0 26.9 + - - +
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Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A HIS* 3.9 29.9 + - - -
68A THR* 4.2 16.5 + - - +
125A ARG* 5.2 2.4 - - - +
128A GLU* 3.0 33.7 + - - +
129A ASP* 2.9 48.4 + - - +
131A GLU* 1.3 74.3 - - + +
133A ASP* 1.3 64.3 + - - +
134A GLY* 3.0 6.4 + - - -
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Residues in contact with ASP 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ASP* 3.1 21.0 + - - +
130A ALA* 4.4 1.4 - - - -
131A GLU 3.3 0.2 - - - -
132A ARG* 1.3 79.6 - - - +
134A GLY* 1.3 56.8 + - - +
135A THR* 3.0 33.1 + - + +
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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