Contacts of the strand formed by residues 295 - 309 (chain A) in PDB entry 1PO3
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 HIS 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A ALA* 4.0 4.5 - - - +
291A PRO* 3.7 25.3 - - + +
292A ASP* 2.9 28.0 + - - +
293A GLU 4.7 0.5 - - - -
294A VAL* 1.3 101.2 + - + +
296A THR* 1.3 64.6 + - - +
297A PHE* 4.3 10.3 - + + -
344A TYR* 3.5 28.3 + + + -
345A GLN 3.8 4.3 - - - -
346A PHE* 4.3 8.9 - + - -
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Residues in contact with THR 296 (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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288A LYS* 4.3 16.7 - - - +
289A TYR 3.1 11.5 + - - -
290A ALA* 4.7 8.1 - - - -
294A VAL 4.1 2.9 - - - +
295A HIS* 1.3 78.0 - - - +
297A PHE* 1.3 70.6 + - - +
298A ASN* 4.7 5.0 + - - +
344A TYR* 2.9 21.4 - - - -
345A GLN* 3.1 58.1 + - + +
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Residues in contact with PHE 297 (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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288A LYS* 3.2 5.8 - - - +
289A TYR* 2.6 67.1 + + + +
291A PRO* 4.6 9.4 - - + -
295A HIS* 4.3 19.5 - + + -
296A THR* 1.3 79.4 + - - +
298A ASN* 1.3 62.5 + - - +
342A LEU* 5.4 10.1 - - + -
343A GLY 3.2 7.4 - - - +
344A TYR* 3.8 38.8 - + + -
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Residues in contact with ASN 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A SER 3.3 10.3 - - - +
288A LYS* 4.1 8.1 - - + +
296A THR* 4.7 5.0 + - - +
297A PHE* 1.3 77.5 - - - +
299A SER* 1.3 60.1 + - - +
341A SER 5.8 0.2 + - - -
342A LEU* 2.9 8.8 - - - +
343A GLY* 2.6 59.9 + - - +
344A TYR* 3.9 3.5 + - - -
345A GLN* 5.1 2.1 + - - +
357A GLN* 4.5 13.5 - - - +
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Residues in contact with SER 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU 4.6 1.8 + - - -
286A LYS* 3.8 8.1 - - - +
287A SER* 2.7 51.2 + - - +
298A ASN* 1.3 78.7 - - - +
300A LEU* 1.3 64.1 + - - +
301A LEU* 5.8 4.4 - - - +
341A SER 3.1 11.7 - - - -
342A LEU* 3.9 11.4 - - - -
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Residues in contact with LEU 300 (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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164A MET* 3.7 23.8 - - + -
165A ASP* 4.3 19.5 - - + +
167A ILE* 4.3 12.6 - - + -
216A THR* 5.1 1.3 - - + -
284A MET* 4.3 19.3 - - + -
285A LEU 3.8 4.7 - - - +
286A LYS* 4.2 27.1 - - + -
299A SER* 1.3 76.7 - - - +
301A LEU* 1.3 75.0 - - - +
339A LEU* 3.5 23.5 - - + +
340A ALA* 3.2 5.0 - - - -
341A SER* 2.7 44.9 + - - +
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A MET* 3.3 4.9 - - - +
285A LEU* 2.8 68.8 + - + +
299A SER* 5.8 4.5 - - - +
300A LEU* 1.3 81.5 - - - +
302A GLN* 1.3 62.2 + - - +
339A LEU 3.1 6.7 - - - +
340A ALA* 4.2 18.8 - - + -
341A SER 5.3 0.2 - - - +
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Residues in contact with GLN 302 (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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164A MET* 3.9 10.5 - - - +
183A PRO 3.6 23.9 + - - +
184A VAL* 4.5 0.6 - - - +
282A ASP* 3.1 26.4 + - - +
283A LEU 3.2 4.0 - - - +
284A MET* 3.5 28.9 - - + -
301A LEU* 1.3 75.4 - - - +
303A TYR* 1.3 67.5 + - - +
304A TYR* 4.1 7.4 - - - +
337A ARG* 3.5 20.9 + - - +
338A LYS* 3.4 8.5 - - - +
339A LEU* 2.7 57.2 + - + +
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Residues in contact with TYR 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ASP* 3.3 6.4 - - + +
283A LEU* 2.4 62.6 + - + +
302A GLN* 1.3 74.3 - - - +
304A TYR* 1.3 60.3 + - - +
305A ASP* 3.7 36.9 + - + -
336A ARG* 6.2 1.8 - - - -
337A ARG 3.7 2.2 - - - -
338A LYS* 4.1 29.8 - - + -
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Residues in contact with TYR 304 (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 ASP 4.1 3.1 + - - -
143A LEU* 3.8 24.6 - - + -
181A LEU* 3.6 22.9 - - + -
182A ALA 3.9 9.5 + - - -
183A PRO* 3.8 20.9 - - + -
184A VAL 3.6 28.7 + - - -
185A SER* 4.2 1.8 - - - -
280A ILE* 3.5 30.7 - - + +
281A ASP 3.3 3.8 - - - -
282A ASP* 3.7 29.8 - - + +
302A GLN* 4.0 5.3 - - - -
303A TYR* 1.3 75.5 - - - +
305A ASP* 1.3 66.8 + - - +
306A GLY* 4.3 2.9 - - - -
335A GLY 4.0 11.2 - - - -
336A ARG* 2.9 3.6 - - - -
337A ARG* 2.6 43.1 + - + +
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Residues in contact with ASP 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ARG* 2.4 46.3 + - - +
280A ILE* 3.8 1.7 - - - +
281A ASP* 2.8 36.7 + - + +
303A TYR* 3.7 33.0 + - + -
304A TYR* 1.3 77.2 - - - +
306A GLY* 1.3 62.0 + - - +
335A GLY 3.4 5.2 - - - -
336A ARG* 4.0 4.7 - - - +
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Residues in contact with GLY 306 (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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143A LEU* 3.7 10.8 - - - -
279A ARG 3.3 10.1 - - - -
280A ILE* 4.4 6.7 - - - -
304A TYR* 4.5 3.4 - - - -
305A ASP* 1.3 84.4 + - - +
307A GLU* 1.3 59.0 + - - -
334A TRP* 2.9 3.5 - - - +
335A GLY 2.4 48.6 + - - -
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Residues in contact with GLU 307 (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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143A LEU* 3.8 4.5 - - - +
277A ALA 4.7 1.3 - - - +
279A ARG* 2.9 71.5 + - + +
306A GLY* 1.3 73.4 - - - -
308A ALA* 1.3 63.7 + - - +
332A ARG* 3.5 28.8 + - - +
333A PHE 3.2 8.3 - - - -
334A TRP* 3.4 17.6 - - + +
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Residues in contact with ALA 308 (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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141A HIS* 3.7 19.3 - - + -
143A LEU* 3.5 17.0 - - + -
277A ALA 3.4 8.3 - - - -
278A THR* 3.4 20.6 - - - +
307A GLU* 1.3 77.1 - - - +
309A ASP* 1.3 62.2 + - - +
310A MET* 3.9 0.4 - - - -
332A ARG* 3.4 9.0 - - - +
333A PHE* 2.6 36.7 + - - +
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Residues in contact with ASP 309 (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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140A SER 4.4 2.1 - - - +
141A HIS* 5.2 0.9 - - - +
275A HIS* 2.8 60.4 + - + +
276A SER* 3.1 12.1 - - - +
277A ALA* 3.2 30.0 + - - +
308A ALA* 1.3 74.5 - - - +
310A MET* 1.3 60.6 + - - +
311A PRO* 3.3 2.9 - - - +
331A ASP 4.2 1.3 - - - -
332A ARG* 3.2 34.1 + - - +
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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