Contacts of the strand formed by residues 213 - 224 (chain B) in PDB entry 1ATH
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 213 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B LEU* 3.8 19.1 - - + -
147B PHE 3.2 35.7 - - - +
148B GLY* 3.8 3.4 - - - +
154B PHE* 4.1 13.9 - - + -
158B TYR* 4.1 23.3 - - + +
170B LEU* 4.6 4.9 - - + -
211B THR* 4.5 2.4 - - - +
212B VAL* 1.3 77.9 - - - +
214B VAL* 1.3 71.7 + - - +
215B LEU* 4.1 10.3 - - + -
354B ILE* 3.6 36.6 - - + -
390B ILE* 2.8 35.8 + - + +
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Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 3.6 2.3 - - - -
147B PHE* 2.9 38.0 + - + +
175B PHE* 4.4 2.9 - - + -
186B ILE* 4.1 12.8 - - + -
202B ILE* 3.6 24.9 - - + -
207B ILE* 3.7 29.2 - - + -
211B THR* 4.0 9.6 - - + -
213B LEU* 1.3 78.0 - - - +
215B LEU* 1.3 70.1 + - - +
216B VAL* 4.1 10.1 - - + -
387B ALA* 4.5 1.3 - - + -
388B VAL 3.1 9.6 - - - +
389B VAL* 3.7 15.7 - - + -
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Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA* 5.2 1.5 - - + +
89B MET* 4.0 17.3 - - + -
90B THR* 3.7 42.4 - - + +
145B ARG 3.9 4.0 - - - -
146B LEU* 3.7 17.7 - - + +
158B TYR* 3.7 18.6 - - - +
213B LEU* 4.3 6.7 - - + -
214B VAL* 1.3 77.2 - - - +
216B VAL* 1.3 59.9 + - - +
386B THR 4.0 0.3 - - - +
387B ALA* 3.3 2.9 - - - -
388B VAL* 2.8 50.3 + - + +
390B ILE* 3.7 31.9 - - + -
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Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA* 5.1 0.4 - - - -
89B MET* 3.3 13.6 - - - +
143B ALA 5.6 0.4 - - - +
144B ASN* 3.5 1.3 - - - -
145B ARG 2.9 35.4 + - - +
147B PHE* 4.3 4.3 - - + -
186B ILE* 4.1 15.9 - - + -
189B TRP* 3.5 32.8 - - + +
190B VAL* 4.0 15.5 - - + -
202B ILE* 4.7 0.4 - - + -
214B VAL* 4.1 11.4 - - + -
215B LEU* 1.3 78.2 - - - +
217B ASN* 1.3 70.8 + - - +
218B THR* 4.5 0.9 - - - +
385B SER* 5.4 0.9 - - - -
386B THR 3.3 3.4 - - - +
387B ALA* 3.7 23.1 - - + -
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Residues in contact with ASN 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B SER* 3.1 34.0 + - - +
85B THR* 3.2 19.9 - - - +
86B ALA* 4.0 24.2 - - + +
142B SER* 3.5 9.7 + - - -
143B ALA 3.6 1.8 + - - -
144B ASN* 2.8 25.9 + - - +
216B VAL* 1.3 75.8 - - - +
218B THR* 1.3 93.2 + - - +
219B ILE* 3.9 2.6 - - - +
385B SER* 3.1 24.8 - - - -
386B THR 2.9 7.9 + - - +
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Residues in contact with THR 218 (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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141B VAL 5.3 0.7 - - - +
142B SER* 2.8 33.0 + - - -
143B ALA* 2.9 23.7 + - + +
189B TRP* 4.9 1.5 + - - -
190B VAL* 4.3 11.6 - - - +
193B LYS* 3.5 41.4 - - + +
194B THR* 3.6 12.3 - - + +
216B VAL* 4.5 3.0 - - - +
217B ASN* 1.3 79.8 + - - +
219B ILE* 1.3 64.8 + - - +
384B ALA 3.3 5.6 - - - -
385B SER* 3.1 14.2 + - - -
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Residues in contact with ILE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B SER* 3.6 12.3 - - - +
81B LEU* 3.6 25.1 - - + -
82B SER* 3.4 31.4 - - - +
85B THR* 5.5 0.7 - - - +
131B TYR* 4.1 9.9 - - + +
140B LEU* 3.8 22.9 - - + -
141B VAL 3.2 11.0 - - - +
142B SER* 4.1 7.6 - - - +
194B THR* 4.3 2.3 - - - +
217B ASN* 3.9 8.1 - - - +
218B THR* 1.3 79.6 - - - +
220B TYR* 1.3 66.5 + - - +
383B ALA* 3.5 4.0 - - - +
384B ALA* 3.1 31.1 + - + +
421B ILE* 5.1 3.6 - - + +
422B PHE* 4.5 15.5 - - + -
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Residues in contact with TYR 220 (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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139B LYS* 3.2 24.5 - - + +
140B LEU* 3.4 3.8 - - - +
141B VAL* 2.8 50.6 + - + +
193B LYS 4.1 14.4 - - - +
194B THR* 4.0 19.3 - - - -
195B GLU* 3.8 27.8 - - + +
197B ARG* 4.7 2.5 - - + -
219B ILE* 1.3 76.5 - - - +
221B PHE* 1.3 62.6 + - - +
222B LYS* 3.8 27.6 - - + +
381B GLU* 3.0 45.8 + - + +
382B ALA 3.5 12.6 - - - -
383B ALA* 4.0 7.0 - - + -
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Residues in contact with PHE 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B SER 4.3 1.6 - - - -
139B LYS 2.9 14.4 - - - +
140B LEU* 4.0 11.2 - - + -
220B TYR* 1.3 79.3 - - - +
222B LYS* 1.3 77.3 + - - +
223B GLY* 3.7 18.4 - - - -
274B PHE* 3.8 28.9 - + - -
279B ILE* 3.5 45.8 - - + -
380B SER* 3.9 14.6 - - - -
381B GLU* 3.4 5.4 - - - +
382B ALA* 2.9 41.5 + - + +
412B ILE* 4.1 20.9 - - + -
421B ILE* 4.9 1.3 - - + -
422B PHE* 3.7 19.5 - + + -
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Residues in contact with LYS 222 (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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138B SER* 3.5 2.3 + - - -
139B LYS* 3.0 45.6 + - + +
220B TYR* 3.8 21.5 - - + +
221B PHE* 1.3 82.1 - - - +
223B GLY* 1.3 61.3 + - - +
224B LEU* 5.3 12.6 - - + -
376B ASN* 5.9 4.5 - - - +
378B GLU* 5.6 3.6 + - - -
379B GLY 6.4 0.4 - - - -
380B SER 3.4 13.0 - - - +
381B GLU* 4.0 21.5 + - + -
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Residues in contact with GLY 223 (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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138B SER* 4.0 9.6 - - - -
221B PHE* 3.7 17.3 - - - -
222B LYS* 1.3 76.2 - - - +
224B LEU* 1.3 67.5 + - - +
274B PHE* 3.5 8.5 - - - -
379B GLY* 3.1 4.2 - - - -
380B SER 3.0 33.2 + - - -
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Residues in contact with LEU 224 (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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138B SER* 5.2 2.2 + - - +
222B LYS* 5.3 12.3 - - + -
223B GLY* 1.3 80.0 - - - +
225B TRP* 1.3 57.5 + - - +
228B LYS* 3.6 19.5 - - - +
274B PHE* 3.2 7.4 - - - +
275B LYS* 2.7 56.1 + - + +
378B GLU* 3.3 50.7 - - + +
379B GLY* 4.6 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