Contacts of the strand formed by residues 172 - 180 (chain B) in PDB entry 1AXI
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 LEU 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B PRO* 3.6 25.6 - - + -
160B PRO* 4.1 25.1 - - + -
163B ALA* 4.4 5.2 - - + -
165B ILE* 3.7 27.5 - - + +
170B MET* 3.9 18.2 - - + -
171B VAL* 1.3 82.9 - - - +
173B GLU* 1.3 62.3 + - - +
174B TYR* 3.7 35.1 - - + +
193B LEU* 4.0 22.9 - - - +
214B SER* 4.4 3.8 - - - -
215B LYS 3.4 17.3 - - - +
216B GLN* 3.9 2.9 - - - +
217B ARG* 4.4 2.9 - - - -
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Residues in contact with GLU 173 (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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172B LEU* 1.3 74.3 - - - +
174B TYR* 1.3 61.5 - - - +
191B PRO* 3.6 18.4 - - + +
192B ILE 3.4 14.8 - - - +
193B LEU* 4.4 10.3 - - + -
214B SER* 3.4 5.5 - - - -
215B LYS* 2.9 55.9 + - + +
217B ARG* 3.9 26.6 - - + +
218B ASN 4.5 3.5 + - - -
222B TYR* 3.1 24.9 + - - +
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Residues in contact with TYR 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PRO* 4.3 12.1 - - + -
157B TRP* 3.5 38.8 - + + -
159B ALA* 3.4 29.4 - - - +
160B PRO* 4.8 0.2 - - + -
165B ILE* 4.2 2.9 - - - +
172B LEU* 3.7 25.6 - - + +
173B GLU* 1.3 76.8 - - - +
175B GLU* 1.3 60.2 + - - +
176B LEU 4.2 0.9 + - - -
190B ASP 4.5 0.3 - - - +
191B PRO* 3.2 5.1 - - - +
192B ILE* 2.9 41.3 + - + +
193B LEU 4.3 9.4 - - - -
194B THR 3.3 18.6 - - - -
195B THR* 3.8 21.4 - - + +
212B VAL* 4.1 3.6 - - + -
213B ARG 3.4 6.5 - - - +
214B SER* 3.9 24.9 - - - -
222B TYR* 4.7 1.3 - - - -
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Residues in contact with GLU 175 (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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174B TYR* 1.3 74.0 - - - +
176B LEU* 1.3 64.1 + - - +
177B GLN* 3.0 25.0 + - + -
188B MET* 3.9 16.6 - - - +
189B MET 3.9 16.4 - - - +
190B ASP 5.1 0.2 - - - -
191B PRO* 4.5 7.8 - - + +
211B ARG 4.1 0.2 - - - +
212B VAL* 3.5 4.5 - - - -
213B ARG* 2.9 66.6 + - + +
222B TYR* 3.8 30.2 - - + +
225B PHE* 4.6 1.7 - - - -
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Residues in contact with LEU 176 (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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155B VAL* 4.0 20.6 - - + -
157B TRP* 4.0 9.9 - - + -
174B TYR 4.2 1.4 + - - -
175B GLU* 1.3 72.7 - - - +
177B GLN* 1.3 79.2 + - - +
178B TYR* 3.9 17.5 - - + -
189B MET* 3.1 56.4 + - + +
190B ASP 5.4 0.2 + - - -
192B ILE* 6.2 0.8 - - + +
197B VAL* 3.8 24.2 - - + -
199B VAL* 4.4 6.5 - - + -
210B VAL* 3.8 25.8 - - + -
211B ARG 3.5 5.6 - - - +
212B VAL* 4.1 9.4 - - + -
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Residues in contact with GLN 177 (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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175B GLU* 3.0 26.0 + - + +
176B LEU* 1.3 84.7 - - - +
178B TYR* 1.3 61.5 + - - +
186B TRP* 3.7 19.7 - - + +
187B LYS 3.3 10.5 - - - +
188B MET* 3.5 25.2 - - + +
210B VAL* 3.4 2.9 - - - -
211B ARG* 2.9 64.9 + - + +
213B ARG* 4.2 4.4 - - - +
225B PHE* 3.3 29.1 - - + -
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Residues in contact with TYR 178 (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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176B LEU* 3.9 16.4 - - + -
177B GLN* 1.3 74.6 - - - +
179B LYS* 1.3 65.0 + - - +
186B TRP* 3.7 5.6 - - - -
187B LYS* 2.8 72.1 + - + +
188B MET 6.2 0.2 - - - -
189B MET* 4.6 15.7 - - + -
199B VAL* 3.8 29.6 - - + +
200B TYR 4.7 6.8 + - - -
202B LEU* 4.0 17.7 - - + -
208B TYR* 4.6 4.9 - + + -
209B GLU 3.2 15.0 - - - +
210B VAL* 3.8 15.3 - - + -
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Residues in contact with LYS 179 (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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178B TYR* 1.3 78.6 - - - +
180B GLU* 1.3 63.2 + - - +
181B VAL 3.6 11.5 + - - -
183B GLU* 2.6 36.5 + - - +
184B THR 4.3 4.0 - - - -
185B LYS 3.4 28.9 - - - +
186B TRP* 3.5 46.4 - - + +
187B LYS* 3.7 7.9 - - - +
208B TYR* 3.5 8.7 - - - -
209B GLU* 3.0 51.7 + - + +
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Residues in contact with GLU 180 (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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179B LYS* 1.3 79.6 + - - +
181B VAL* 1.3 67.2 + - - +
182B ASN* 3.0 47.1 + - - +
183B GLU* 2.8 45.4 + - - +
187B LYS* 5.0 0.7 - - - +
206B LYS* 3.8 39.4 + - + +
207B GLU 3.5 17.2 + - - +
208B TYR* 3.8 16.7 - - + +
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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