Contacts of the helix formed by residues 147 - 156 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A ASN 5.2 1.4 + - - +
147A THR* 4.3 10.7 - - + +
150A GLU* 4.2 8.9 + - - +
404A PRO* 4.3 6.1 - - + -
146B MET* 1.3 82.4 - - - +
148B MET* 1.3 63.8 + - - +
149B LYS* 3.3 8.3 + - - +
150B GLU* 3.1 24.6 + - - +
151B LEU* 3.1 18.0 + - - +
177B THR 3.6 8.7 - - - -
178B HIS* 3.3 23.2 - - + +
180B VAL 3.1 12.6 - - - +
182B ALA 4.0 2.0 - - - -
404B PRO* 3.9 23.6 - - + -
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Residues in contact with MET 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B MET* 4.1 17.3 - - + -
147B THR* 1.3 73.7 - - - +
149B LYS* 1.3 58.3 + - - +
151B LEU* 3.3 14.7 + - + +
152B LEU* 2.9 61.3 + - + +
169B VAL* 4.1 10.8 - - + -
177B THR* 3.1 20.1 + - - +
180B VAL* 3.0 22.0 + - + -
182B ALA* 3.8 25.8 - - - +
185B PHE* 3.5 46.4 - - + -
186B LEU* 4.7 2.0 - - - -
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Residues in contact with LYS 149 (chain B).
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* 4.0 24.5 - - + +
150A GLU* 5.8 3.8 - - - +
147B THR* 3.1 8.2 - - - +
148B MET* 1.3 76.8 - - - +
150B GLU* 1.3 57.1 + - - +
152B LEU* 3.3 5.4 + - - +
153B ASP* 2.9 53.9 + - - +
162B LYS* 6.3 0.6 - - - +
177B THR* 3.0 29.2 + - - +
178B HIS* 3.8 25.4 + - + +
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Residues in contact with GLU 150 (chain B).
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* 5.9 2.3 - - - +
150A GLU* 3.8 35.2 + - - +
153A ASP* 4.8 8.0 - - - +
145B ASN 4.8 1.4 - - - +
146B MET* 3.4 33.7 - - + +
147B THR* 3.1 22.4 + - - +
149B LYS* 1.3 76.0 - - - +
151B LEU* 1.3 63.8 + - - +
153B ASP* 3.3 11.0 + - + +
154B LYS* 3.1 40.7 + - + +
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B MET* 5.1 1.8 - - - -
125B MET* 4.0 33.9 - - + -
143B TRP* 6.1 0.2 - - + -
146B MET* 3.8 20.5 - - + +
147B THR 3.1 13.1 + - - +
148B MET* 3.7 31.9 - - + +
150B GLU* 1.3 77.6 - - - +
152B LEU* 1.3 57.4 + - + +
154B LYS* 3.2 8.5 + - + +
155B LEU* 2.9 55.6 + - + +
182B ALA* 4.1 10.3 - - + -
186B LEU* 4.0 14.8 - - + -
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B PHE* 3.4 36.1 - - + -
148B MET* 2.9 37.3 + - + +
149B LYS* 3.8 4.7 - - + +
151B LEU* 1.3 75.2 - - + +
153B ASP* 1.3 58.7 + - - +
155B LEU* 4.4 2.0 - - + +
156B CYS* 2.9 38.5 + - - +
162B LYS* 4.1 15.9 - - + +
165B ALA* 3.7 20.6 - - + +
166B THR* 3.7 24.0 - - - +
169B VAL* 4.8 2.2 - - + -
177B THR* 3.9 20.9 - - + -
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Residues in contact with ASP 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLU* 5.5 2.4 - - - +
149B LYS* 2.9 46.6 + - - +
150B GLU* 3.6 10.1 - - + +
152B LEU* 1.3 79.8 - - - +
154B LYS* 1.3 61.3 + - + +
156B CYS 4.0 2.3 - - - +
162B LYS* 3.0 33.7 + - - +
1502B C15 3.4 28.4 - - - -
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Residues in contact with LYS 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B MET* 3.6 27.6 - - + -
150B GLU* 3.1 36.3 + - + +
151B LEU* 3.5 11.2 - - + +
153B ASP* 1.3 77.2 - - + +
155B LEU* 1.3 67.4 + - + +
157B TRP* 4.0 4.0 + - - -
1502B C15 3.3 47.0 + - + +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ASP* 3.6 5.9 - - - +
117B ASN* 4.6 15.5 - - - +
118B PHE* 4.7 21.7 - - + +
121B THR* 3.8 38.1 - - + +
122B MET* 5.5 2.9 - - - -
125B MET* 4.7 2.9 - - - -
151B LEU* 2.9 47.6 + - + +
152B LEU* 4.4 2.5 - - + +
154B LYS* 1.3 80.1 - - + +
156B CYS* 1.3 69.8 + - - +
157B TRP* 3.5 13.4 + - - -
490B PRO* 5.7 0.2 - - - +
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Residues in contact with CYS 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ASP* 3.7 6.5 - - - +
118B PHE* 4.2 26.2 - - - -
152B LEU* 2.9 28.2 + - - +
153B ASP 4.0 4.5 - - - +
155B LEU* 1.3 77.1 - - - +
157B TRP* 1.3 63.1 + - - +
158B THR 3.3 16.7 + - - +
161B ALA* 4.0 12.1 - - - -
162B LYS* 3.9 36.3 + - + +
165B ALA* 4.6 0.2 - - - -
1502B C15 3.5 12.2 - - - -
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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