Contacts of the helix formed by residues 147 - 160 (chain A) in PDB entry 2FE2
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 ALA 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A PHE* 4.2 22.2 - - + -
146A GLY* 1.4 76.5 - - - -
148A LYS* 1.3 65.4 + - + +
149A LYS* 3.3 8.7 - - + +
150A ALA* 3.3 6.1 + - - +
151A VAL* 3.2 22.3 + - - +
201A LYS* 5.1 1.3 - - - -
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Residues in contact with LYS 148 (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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147A ALA* 1.3 72.3 - - + +
149A LYS* 1.3 86.4 + - + +
151A VAL* 2.7 31.5 - - + +
152A LYS* 2.8 13.8 + - - +
201A LYS* 5.3 4.2 - - - +
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Residues in contact with LYS 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 5.0 8.9 - - + +
100A GLY* 4.8 3.4 + - - -
103A ALA* 4.9 6.2 - - - +
104A SER* 4.1 35.5 + - - +
107A PHE* 4.0 28.0 - - + -
147A ALA* 3.3 2.8 - - + +
148A LYS* 1.3 103.8 - - + +
150A ALA* 1.3 53.3 + - - +
152A LYS* 3.1 8.8 + - + +
153A LYS* 2.7 38.4 + - - +
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Residues in contact with ALA 150 (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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107A PHE* 3.2 27.5 - - + -
108A LYS 4.7 2.5 - - - +
110A ASN* 5.6 3.6 - - + +
146A GLY* 5.1 3.6 - - - -
147A ALA 3.3 16.6 + - - +
148A LYS 3.2 0.2 - - - -
149A LYS* 1.3 80.2 - - - +
151A VAL* 1.3 62.2 + - + +
153A LYS* 2.7 38.1 - - + +
154A THR* 3.0 6.2 + - - +
198A LYS* 4.2 19.1 - - + -
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Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLY* 5.2 2.5 - - - -
147A ALA 3.2 10.3 + - - +
148A LYS* 2.7 33.0 + - + +
150A ALA* 1.3 77.4 - - + +
152A LYS* 1.3 62.8 + - + +
154A THR* 3.0 0.9 + - - -
155A PRO* 2.7 34.3 - - - +
198A LYS* 4.7 3.8 - - - +
201A LYS* 3.2 35.0 - - + -
202A PRO* 3.1 34.8 - - + -
205A ALA* 6.0 3.6 - - + -
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Residues in contact with LYS 152 (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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56A ARG* 4.1 19.8 - - - +
91A SER* 4.4 20.1 + - - -
95A LEU* 3.9 38.6 - - + -
104A SER* 4.6 3.6 - - - +
148A LYS* 2.8 17.7 + - + +
149A LYS* 3.6 10.8 - - + +
151A VAL* 1.3 81.1 - - - +
153A LYS* 1.3 62.4 + - - +
155A PRO* 3.3 8.3 - - + +
156A LYS* 3.0 21.0 + - + +
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Residues in contact with LYS 153 (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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104A SER* 3.3 29.1 + - - +
105A GLY* 4.5 9.2 - - - -
107A PHE* 4.2 20.4 - - + +
109A LEU* 4.6 4.7 - - - +
149A LYS 2.7 19.5 + - - +
150A ALA* 2.7 35.4 - - - +
152A LYS* 1.3 74.5 - - - +
154A THR* 1.3 93.1 + - + +
156A LYS* 3.2 17.0 + - - +
157A LYS* 3.0 36.6 + - - +
198A LYS* 3.4 21.2 - - + +
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Residues in contact with THR 154 (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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150A ALA 3.0 2.7 + - - +
151A VAL 3.0 1.2 + - - -
153A LYS* 1.3 97.9 - - + +
155A PRO* 1.3 74.4 - - - +
157A LYS* 3.4 1.9 + - - -
158A ALA 3.0 13.9 + - - -
175A LYS* 2.8 38.0 + - - +
198A LYS* 3.0 52.6 + - + +
199A ALA* 4.4 0.9 - - - +
202A PRO* 2.9 20.1 - - - +
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Residues in contact with PRO 155 (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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88A SER* 4.5 12.5 - - - +
91A SER* 5.4 8.5 - - - +
151A VAL 2.7 24.9 - - - +
152A LYS* 3.8 7.4 - - + +
153A LYS 3.3 0.2 - - - -
154A THR* 1.3 88.6 - - - +
156A LYS* 1.3 66.3 + - - +
158A ALA* 3.6 6.6 - - + +
159A LYS* 2.9 22.9 + - - +
175A LYS* 3.9 4.5 - - + -
202A PRO* 3.1 24.2 - - + -
205A ALA* 6.1 1.1 - - + -
206A LYS* 4.3 21.3 - - + +
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Residues in contact with LYS 156 (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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91A SER* 5.2 2.2 - - - -
92A LYS* 3.8 29.9 - - + +
95A LEU* 3.2 46.7 - - + -
101A THR* 3.6 26.2 - - + +
104A SER* 3.0 35.2 + - - +
105A GLY* 3.5 13.1 - - - +
152A LYS* 3.0 19.3 + - + +
153A LYS* 3.2 18.8 + - - +
155A PRO* 1.3 76.9 - - - +
157A LYS* 1.3 66.7 + - - +
159A LYS* 3.1 16.1 + - - +
160A LYS* 3.8 3.3 + - - +
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Residues in contact with LYS 157 (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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105A GLY* 6.5 0.4 - - - -
153A LYS* 3.0 26.2 + - - +
154A THR* 3.8 5.4 - - - +
156A LYS* 1.3 83.6 - - - +
158A ALA* 1.4 51.0 + - - +
160A LYS* 3.2 10.4 + - + +
161A PRO* 2.8 31.7 - - + +
175A LYS* 5.0 2.9 - - - +
193A LYS* 6.6 0.4 - - - +
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Residues in contact with ALA 158 (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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154A THR 3.0 7.8 + - - +
155A PRO 3.6 1.6 - - - +
157A LYS* 1.4 69.8 - - - +
159A LYS* 1.3 66.6 + - - +
160A LYS 3.1 2.5 - - - -
161A PRO* 2.8 26.1 - - - +
174A LYS* 4.1 12.6 - - + +
175A LYS* 3.3 34.1 - - - +
176A ALA* 4.5 8.7 - - + +
206A LYS* 3.6 20.4 - - - +
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Residues in contact with LYS 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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85A GLY 5.4 0.2 - - - +
88A SER* 3.7 11.7 - - - +
89A LEU* 3.1 63.0 - - + +
92A LYS* 3.6 28.3 - - + +
93A GLY* 5.6 0.6 - - - +
155A PRO 2.9 12.7 + - - +
156A LYS 3.2 13.2 - - - +
158A ALA* 1.3 78.7 - - - +
160A LYS* 1.3 61.9 + - + +
161A PRO 4.1 4.5 - - - +
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Residues in contact with LYS 160 (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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156A LYS 3.8 2.9 + - - +
157A LYS* 3.2 8.6 + - + +
159A LYS* 1.3 83.9 - - + +
161A PRO* 1.3 74.4 - - + +
162A ALA 3.6 0.9 + - - -
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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