Contacts of the helix formed by residues 112 - 128 (chain A) in PDB entry 5L0P
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 112 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A HIS* 5.9 0.3 - - - -
110A TYR 3.3 3.8 + - - -
111A TRP* 1.3 75.5 - - - +
113A ARG* 1.3 62.8 + - - +
114A ASP* 3.3 11.0 + - - +
115A ASP* 3.0 32.8 + - - -
116A VAL* 3.0 21.8 + - - +
140A ASN* 4.0 6.7 - - - -
213A SER* 5.8 0.2 - - - -
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Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER* 1.3 72.7 - - - +
114A ASP* 1.3 68.2 + - - +
116A VAL* 3.3 4.3 + - - +
117A ALA* 3.2 20.4 + - - +
137A PHE 5.1 1.4 - - - +
138A GLU* 3.6 30.0 + - - +
139A MET 3.5 27.1 - - - +
140A ASN* 3.7 6.8 - - - +
213A SER* 2.9 44.3 + - - +
214A LEU 3.8 15.4 + - - -
215A ARG* 3.4 27.3 - - - +
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Residues in contact with ASP 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER* 3.2 9.6 + - - +
113A ARG* 1.3 83.7 - - - +
115A ASP* 1.4 65.4 + - - +
117A ALA* 3.1 9.7 + - - +
118A GLN* 2.9 28.4 + - + +
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Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A HIS* 3.2 37.8 + - - +
104A LEU* 3.6 23.0 - - + +
106A LEU* 5.2 3.1 - - - +
110A TYR 4.2 2.3 - - - +
111A TRP* 3.4 22.6 - - + -
112A SER* 3.0 38.2 + - - +
114A ASP* 1.4 73.9 - - - +
116A VAL* 1.3 54.1 + - - +
118A GLN* 3.0 8.2 + - - +
119A TRP* 2.6 36.4 + - - +
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A TRP* 4.2 7.4 - - + -
112A SER 3.0 15.1 + - - +
113A ARG 3.6 7.6 - - - +
114A ASP 3.3 0.2 - - - -
115A ASP* 1.3 73.8 - - - +
117A ALA* 1.3 58.9 + - - +
119A TRP* 2.9 28.7 + - + +
120A LEU* 2.9 17.1 + - + +
137A PHE* 3.8 35.0 - - + +
139A MET* 3.5 17.3 - - + +
140A ASN 3.7 2.7 - - - +
141A GLY* 3.6 23.8 - - - +
144A LEU* 4.1 22.4 - - + -
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Residues in contact with ALA 117 (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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113A ARG 3.2 9.0 + - - +
114A ASP* 3.1 12.5 + - - +
116A VAL* 1.3 80.8 - - - +
118A GLN* 1.3 68.8 + - - +
120A LEU* 3.3 14.4 + - - +
121A LYS* 3.1 22.5 + - - +
134A SER* 4.8 18.8 - - - +
137A PHE 6.1 0.7 - - - +
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Residues in contact with GLN 118 (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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101A PRO* 5.2 3.6 - - + +
104A LEU* 4.2 11.8 - - + +
114A ASP* 2.9 20.7 + - + +
115A ASP* 3.6 9.2 - - - +
117A ALA* 1.3 80.8 - - - +
119A TRP* 1.3 64.4 + - - +
121A LYS* 3.4 35.1 + - - +
122A TRP* 3.0 24.4 + - - +
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Residues in contact with TRP 119 (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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100A LEU* 4.2 17.0 - - + +
104A LEU* 3.7 12.3 - - + +
111A TRP* 3.5 37.0 - + + -
115A ASP 2.6 15.6 + - - +
116A VAL* 2.9 16.8 + - + +
118A GLN* 1.3 73.1 - - - +
120A LEU* 1.3 85.6 + - + +
122A TRP* 3.7 4.6 - + - +
123A ALA* 2.9 29.4 + - + +
137A PHE* 5.7 0.9 - + - -
144A LEU* 4.0 22.7 - - + -
152A PHE* 4.1 19.3 - + - -
163A LEU* 3.7 33.7 - - + -
166A LEU* 3.6 25.0 - - + +
167A LEU* 4.0 15.7 - - + -
170A ILE* 3.5 18.2 - - - +
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Residues in contact with LEU 120 (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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116A VAL* 2.9 19.0 + - + +
117A ALA* 3.5 14.1 - - - +
118A GLN 3.2 0.2 - - - -
119A TRP* 1.3 102.8 - - + +
121A LYS* 1.3 60.4 + - - +
123A ALA* 3.2 5.2 + - - +
124A GLU* 2.9 31.8 + - - +
132A ILE* 3.7 32.9 - - + +
133A ASP 4.4 4.7 - - - +
134A SER* 5.0 7.4 - - - +
136A THR* 4.4 4.9 - - - -
137A PHE* 3.9 38.8 - - + +
163A LEU* 4.1 17.5 - - + -
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Residues in contact with LYS 121 (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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117A ALA 3.1 12.7 + - - +
118A GLN* 3.4 34.6 + - - +
119A TRP 3.4 0.2 - - - -
120A LEU* 1.3 78.3 - - - +
122A TRP* 1.3 65.4 + - - +
124A GLU* 3.4 8.0 + - - +
125A ASN* 3.0 38.3 + - - +
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Residues in contact with TRP 122 (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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98A ILE* 4.3 16.6 - - + -
99A ARG 3.7 21.5 + - - -
100A LEU* 3.6 25.6 - - + -
101A PRO* 3.4 38.6 - - + +
118A GLN 3.0 18.3 + - - +
119A TRP* 3.7 11.4 - + - +
121A LYS* 1.3 77.1 - - - +
123A ALA* 1.3 74.1 + - + +
125A ASN* 3.2 8.6 + - + +
126A GLU* 2.8 62.7 + - + +
127A PHE* 4.0 22.2 - + - -
166A LEU* 4.1 12.8 - - + -
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Residues in contact with ALA 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 TRP* 2.9 19.8 + - - +
120A LEU 3.2 4.7 + - - +
122A TRP* 1.3 86.3 - - + +
124A GLU* 1.3 60.0 + - - +
127A PHE* 3.1 36.8 + - + +
129A LEU* 3.9 2.9 - - + +
132A ILE* 5.1 0.2 - - + -
163A LEU* 3.8 19.7 - - + -
166A LEU* 3.6 28.5 - - + -
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Residues in contact with GLU 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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120A LEU 2.9 19.9 + - - +
121A LYS* 3.9 7.9 - - - +
123A ALA* 1.3 71.9 - - - +
125A ASN* 1.3 61.8 + - - +
128A SER* 3.1 9.7 + - - -
129A LEU* 3.1 42.4 + - + +
130A ARG 4.0 2.0 - - - +
131A PRO* 3.5 18.5 - - - +
132A ILE* 2.7 46.0 + - + +
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Residues in contact with ASN 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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54A ASN* 5.2 0.2 + - - -
121A LYS* 3.0 33.1 + - - +
122A TRP* 3.2 9.9 + - + +
124A GLU* 1.3 77.5 - - - +
126A GLU* 1.3 66.2 + - - +
127A PHE 3.1 2.3 + - - -
128A SER* 3.7 8.5 + - - +
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Residues in contact with GLU 126 (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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54A ASN* 3.0 16.0 + - - -
56A LYS* 3.0 35.9 + - - +
122A TRP* 2.8 51.8 + - + +
123A ALA* 3.3 0.6 + - - -
125A ASN* 1.3 74.4 - - - +
127A PHE* 1.3 90.2 + - + +
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Residues in contact with PHE 127 (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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53A MET* 3.6 4.2 - - - +
54A ASN* 3.1 26.1 + - - +
56A LYS* 3.9 25.8 - - + -
57A ALA* 3.6 30.7 - - + -
60A LEU* 4.0 21.3 - - + -
98A ILE* 4.6 11.0 - - + -
122A TRP* 4.0 7.6 - + - -
123A ALA* 3.1 30.6 + - + +
126A GLU* 1.3 105.3 - - + +
128A SER* 1.4 69.8 + - - +
129A LEU* 3.3 13.9 + - + +
162A VAL* 4.7 6.1 - - + -
166A LEU* 3.9 31.6 - - + -
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Residues in contact with SER 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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27A ARG* 2.8 47.2 + - - +
52A GLU 3.6 2.3 - - - +
54A ASN* 3.6 18.4 + - - +
124A GLU 3.1 9.6 + - - -
125A ASN 3.7 6.0 + - - -
126A GLU 3.6 1.6 - - - -
127A PHE* 1.4 79.0 - - - +
129A LEU* 1.3 61.6 + - - +
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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