Contacts of the helix formed by residues 158 - 173 (chain A) in PDB entry 5LPN
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 ASN 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A PHE* 3.7 24.8 - - + -
150A GLU* 2.9 28.0 + - - +
151A THR* 3.8 8.0 - - + +
156A ASN 3.6 3.8 + - - -
157A ILE* 1.3 80.2 - - - +
159A ILE* 1.3 64.2 + - - +
160A GLU 3.6 1.1 - - - -
161A LYS* 4.1 21.2 - - - +
162A ALA* 3.2 24.1 + - - +
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Residues in contact with ILE 159 (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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25A VAL* 3.7 42.0 - - + +
28A ARG* 3.5 28.5 - - + -
29A PHE* 3.6 30.5 - - + -
120A LEU* 6.1 0.2 - - + -
151A THR* 4.0 16.6 - - + -
152A SER 3.8 7.9 - - - +
153A ALA* 4.1 10.5 - - - +
156A ASN* 4.4 8.8 + - - +
157A ILE 3.2 8.0 - - - +
158A ASN* 1.3 76.6 - - - +
160A GLU* 1.3 69.0 + - - +
162A ALA* 3.5 2.4 - - - +
163A PHE* 3.1 32.2 + - + -
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Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 4.1 24.2 - - + -
49A LYS* 4.7 8.5 + - - -
156A ASN* 5.1 5.1 + - - +
159A ILE* 1.3 79.1 - - - +
161A LYS* 1.3 57.9 + - - +
163A PHE* 3.2 2.4 + - - +
164A LEU* 2.9 56.7 + - + +
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Residues in contact with LYS 161 (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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149A PHE* 3.6 30.6 - - + -
158A ASN* 3.8 21.6 + - - +
159A ILE 3.2 1.0 - - - -
160A GLU* 1.3 77.9 - - - +
162A ALA* 1.3 59.1 + - - +
164A LEU* 4.2 5.2 - - - +
165A THR* 2.6 44.9 + - - +
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Residues in contact with ALA 162 (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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86A MET* 4.0 6.1 - - + -
118A MET* 3.3 18.0 - - - +
120A LEU* 4.0 16.8 - - + -
149A PHE* 3.5 31.3 - - + -
151A THR* 4.7 0.9 - - + -
158A ASN 3.2 21.7 + - - +
159A ILE* 3.2 4.2 + - - +
161A LYS* 1.3 76.9 - - - +
163A PHE* 1.3 63.1 + - + +
165A THR* 3.3 1.0 + - - -
166A LEU* 3.0 20.1 + - - +
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Residues in contact with PHE 163 (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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12A LEU* 4.2 15.1 - - + +
14A LEU* 3.9 22.9 - - + -
25A VAL* 3.8 27.6 - - + -
26A LEU* 4.6 6.1 - - + -
29A PHE* 3.7 46.7 - + + -
60A LEU* 4.9 3.4 - - + +
62A ILE* 3.6 40.6 - - + -
86A MET* 3.5 22.7 - - + -
120A LEU* 5.5 0.7 - - + -
159A ILE* 3.1 21.3 + - + -
160A GLU 3.8 2.0 - - - +
162A ALA* 1.3 79.1 - - + +
164A LEU* 1.3 58.7 + - - +
166A LEU* 3.2 4.5 + - - +
167A ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 164 (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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29A PHE* 4.7 10.1 - - + -
51A VAL* 3.8 34.3 - - + -
52A GLU 5.7 3.4 - - - +
53A LEU* 4.0 16.9 - - + +
60A LEU* 5.3 1.1 - - + -
160A GLU* 2.9 42.5 + - + +
161A LYS* 4.2 4.7 - - - +
163A PHE* 1.3 78.1 - - - +
165A THR* 1.3 57.8 + - - +
167A ALA* 3.8 4.7 - - + +
168A GLU* 2.8 38.0 + - - +
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Residues in contact with THR 165 (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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118A MET* 3.6 18.4 - - + -
147A ARG* 3.7 27.1 - - - +
149A PHE* 4.1 11.3 - - + -
161A LYS* 2.6 35.9 + - - +
162A ALA 3.5 4.0 - - - -
164A LEU* 1.3 74.3 - - - +
166A LEU* 1.3 60.4 + - - +
168A GLU* 3.3 6.5 + - - +
169A ASP* 2.9 36.7 + - - +
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Residues in contact with LEU 166 (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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12A LEU* 3.7 34.5 - - + -
84A GLY* 4.0 16.4 - - - -
85A ILE 4.2 1.8 - - - +
86A MET* 3.7 32.3 - - + -
116A GLU* 3.8 30.7 - - + +
117A ARG 5.1 0.4 - - - -
118A MET* 3.6 23.7 - - + +
162A ALA 3.0 13.7 + - - +
163A PHE 3.5 7.4 - - - +
165A THR* 1.3 76.8 - - - +
167A ALA* 1.3 55.5 + - - +
169A ASP* 3.1 7.8 + - + +
170A ILE* 2.9 34.7 + - + +
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Residues in contact with ALA 167 (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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10A PHE* 3.5 13.2 - - + -
12A LEU* 5.5 3.3 - - + +
51A VAL* 4.9 1.6 - - + -
53A LEU* 3.6 22.4 - - + -
60A LEU* 4.1 27.4 - - + -
163A PHE 2.9 16.4 + - - +
164A LEU* 3.8 6.1 - - - +
166A LEU* 1.3 77.1 - - - +
168A GLU* 1.3 58.3 + - - +
170A ILE* 3.5 2.6 + - - -
171A LEU* 2.8 31.0 + - - +
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Residues in contact with GLU 168 (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 LEU* 3.6 27.3 - - + +
54A GLN* 6.5 1.1 - - - -
164A LEU* 2.8 26.1 + - - +
165A THR* 3.7 7.4 - - - +
167A ALA* 1.3 72.5 - - - +
169A ASP* 1.3 61.9 + - - +
171A LEU* 3.7 9.0 - - + +
172A ARG* 2.9 30.7 + - - +
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Residues in contact with ASP 169 (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 GLU* 4.0 25.3 - - + +
118A MET* 4.4 3.3 - - - +
147A ARG* 3.1 49.0 + - - +
165A THR* 2.9 27.7 + - - +
166A LEU* 3.1 7.6 + - + +
168A GLU* 1.3 78.9 - - - +
170A ILE* 1.3 65.3 + - - +
172A ARG* 3.3 15.2 + - - +
173A LYS* 3.5 14.3 - - - +
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Residues in contact with ILE 170 (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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10A PHE* 4.0 17.5 - - + -
12A LEU* 3.5 24.9 - - + -
83A MET* 3.3 69.3 - - + +
84A GLY* 3.6 3.4 - - - +
116A GLU* 4.3 10.3 - - + -
166A LEU* 2.9 20.9 + - + +
167A ALA* 3.8 3.6 - - - +
169A ASP* 1.3 75.3 - - - +
171A LEU* 1.3 63.6 + - - +
172A ARG 3.1 0.7 + - - -
173A LYS* 3.2 27.5 + - - +
174A THR* 3.2 10.6 - - - +
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Residues in contact with LEU 171 (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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8A LEU* 4.2 12.3 - - + -
10A PHE* 3.7 12.7 - - + -
53A LEU* 4.2 26.2 - - + +
54A GLN* 6.3 0.7 - - + -
56A LYS* 4.4 15.5 - - + -
58A ILE* 3.6 26.9 - - + -
167A ALA 2.8 21.9 + - - +
168A GLU* 3.7 7.6 - - + +
170A ILE* 1.3 73.8 - - - +
172A ARG* 1.3 61.6 + - - +
174A THR* 2.2 42.0 + - - +
175A PRO* 4.4 0.5 - - - +
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Residues in contact with ARG 172 (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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168A GLU 2.9 17.7 + - - +
169A ASP* 3.6 7.6 - - - +
170A ILE 3.1 0.8 + - - -
171A LEU* 1.3 78.5 - - - +
173A LYS* 1.3 60.8 + - + +
174A THR 3.3 2.8 + - - -
175A PRO* 4.0 8.3 - - - +
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Residues in contact with LYS 173 (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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83A MET 5.6 1.1 - - - -
114A ASP* 2.8 38.7 + - - +
115A VAL* 4.7 0.4 - - - +
116A GLU* 2.8 43.9 + - - +
169A ASP 3.5 9.0 - - - +
170A ILE* 3.2 18.5 + - - +
172A ARG* 1.3 79.2 - - + +
174A THR* 1.3 57.8 + - - +
175A PRO* 3.8 3.0 - - - -
1053B GLU* 4.8 5.5 - - - +
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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
------------------------------------------------------------
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