Contacts of the helix formed by residues 147 - 156 (chain A) in PDB entry 2XFN
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 THR 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A MET* 1.3 77.4 - - - +
148A MET* 1.3 64.6 + - - +
149A LYS* 3.2 9.2 + - - +
150A GLU* 3.0 36.4 + - - +
151A LEU 3.1 16.6 + - - -
177A THR 3.6 9.2 - - - -
178A HIS* 3.4 23.0 - - + +
180A VAL 3.1 11.0 - - - +
182A ALA* 3.9 6.6 - - - +
404A PRO* 3.8 23.1 - - + -
145B ASN 5.2 2.6 + - - +
146B MET* 6.3 0.4 - - - -
147B THR* 4.3 6.3 - - + +
404B PRO* 4.2 6.5 - - + -
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Residues in contact with MET 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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118A PHE* 5.4 0.2 - - + -
122A MET* 3.9 19.3 - - + -
147A THR* 1.3 73.3 - - - +
149A LYS* 1.3 57.1 + - - +
151A LEU* 3.2 18.8 + - + +
152A LEU* 2.9 57.4 + - + +
169A VAL* 4.0 12.6 - - + -
177A THR* 3.2 18.1 + - + +
180A VAL* 2.9 23.8 + - + -
182A ALA* 3.7 22.2 - - - +
185A PHE* 3.5 46.4 - - + -
186A LEU* 4.8 1.1 - - - -
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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
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147A THR* 3.1 9.6 - - - +
148A MET* 1.3 74.6 - - - +
150A GLU* 1.3 58.8 + - + +
152A LEU* 3.2 6.6 + - + +
153A ASP* 2.9 51.3 + - - +
177A THR* 3.0 30.9 + - - +
178A HIS* 3.7 26.1 + - + +
145B ASN* 4.2 27.4 - - + +
150B GLU* 5.9 2.7 - - - +
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Residues in contact with GLU 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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145A ASN 4.3 2.8 - - - +
146A MET* 3.4 27.3 - - + +
147A THR* 3.0 40.5 + - - +
149A LYS* 1.3 77.3 - - + +
151A LEU* 1.3 63.1 + - - +
153A ASP* 3.3 10.6 + - - +
154A LYS* 3.1 28.8 + - - +
147B THR* 4.2 12.9 + - - +
149B LYS* 5.8 3.5 - - - +
150B GLU* 3.8 40.3 + - - +
153B ASP* 5.5 2.6 - - - +
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Residues in contact with LEU 151 (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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122A MET* 4.7 2.0 - - - -
125A MET* 4.1 22.0 - - + -
146A MET* 3.4 21.0 - - + +
147A THR 3.1 10.5 + - - +
148A MET* 3.7 32.5 - - + +
150A GLU* 1.3 76.7 - - - +
152A LEU* 1.3 61.7 + - + +
154A LYS* 3.2 9.0 + - + +
155A LEU* 2.9 52.5 + - + +
182A ALA* 4.1 8.7 - - + -
186A LEU* 4.0 26.7 - - + -
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Residues in contact with LEU 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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118A PHE* 3.3 36.3 - - + -
122A MET* 5.3 0.2 - - - -
148A MET* 2.9 33.0 + - + +
149A LYS* 3.7 5.6 - - + +
151A LEU* 1.3 77.8 - - + +
153A ASP* 1.3 58.8 + - - +
155A LEU* 4.4 1.3 - - + +
156A CYS* 2.9 39.2 + - - +
162A LYS* 4.1 16.9 - - + +
165A ALA* 3.6 21.5 - - + +
166A THR* 3.6 27.1 - - - +
169A VAL* 4.9 1.3 - - + -
177A THR* 4.0 18.4 - - + -
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Residues in contact with ASP 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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149A LYS* 2.9 40.5 + - - +
150A GLU* 3.6 12.8 - - - +
151A LEU 3.2 0.2 - - - -
152A LEU* 1.3 77.2 - - - +
154A LYS* 1.3 61.0 + - + +
156A CYS 4.1 1.9 - - - +
162A LYS* 2.9 34.2 + - - +
1502A C15 3.4 29.7 - - - -
150B GLU* 4.8 9.0 - - - +
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Residues in contact with LYS 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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142A GLU* 5.2 7.7 + - - +
146A MET* 3.7 33.4 - - + +
150A GLU* 3.1 14.5 + - - +
151A LEU* 3.5 13.7 - - + +
152A LEU 3.1 0.2 - - - -
153A ASP* 1.3 79.2 - - + +
155A LEU* 1.3 64.5 + - + +
157A TRP* 3.9 4.3 + - - -
1502A C15 3.4 40.9 + - + +
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Residues in contact with LEU 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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114A ASP* 3.6 6.6 - - - +
117A ASN* 4.5 14.9 - - - +
118A PHE* 4.3 26.1 - - + +
121A THR* 3.9 36.6 - - + +
122A MET* 5.0 4.3 - - - -
125A MET* 4.7 2.5 - - - -
151A LEU* 2.9 48.0 + - + +
152A LEU* 4.4 1.3 - - - +
154A LYS* 1.3 80.5 - - + +
156A CYS* 1.3 69.1 + - - +
157A TRP* 3.5 13.3 + - - -
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Residues in contact with CYS 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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114A ASP* 3.8 7.0 - - - +
118A PHE* 3.9 29.2 - - - -
152A LEU* 2.9 28.5 + - - +
153A ASP 4.1 3.5 - - - +
154A LYS 3.6 0.2 - - - -
155A LEU* 1.3 76.5 - - - +
157A TRP* 1.3 61.4 + - - +
158A THR 3.3 20.1 + - - +
161A ALA* 4.0 10.3 - - - -
162A LYS* 3.8 35.4 + - + +
1502A C15 3.5 12.5 - - - -
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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