Contacts of the helix formed by residues 325 - 336 (chain A) in PDB entry 1XPU
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 SER 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A ARG* 4.0 12.6 + - - -
323A THR* 3.5 3.9 + - - -
324A GLY* 1.3 79.2 + - - +
326A LYS* 1.3 64.2 + - - +
327A MET* 3.8 15.8 + - - +
328A ASP* 3.1 37.9 + - - +
329A GLU* 3.6 6.9 + - - +
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Residues in contact with LYS 326 (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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287A GLY* 4.5 6.7 - - - +
324A GLY 4.1 4.4 + - - +
325A SER* 1.3 70.2 + - - +
327A MET* 1.3 64.6 + - - +
329A GLU* 3.1 29.3 + - + +
330A VAL* 3.2 19.5 + - + +
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Residues in contact with MET 327 (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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272A ARG* 2.9 45.8 - - - +
275A ASN* 3.6 21.8 - - - +
276A THR* 6.3 0.4 - - + -
287A GLY 3.9 15.2 + - - +
288A GLY* 3.4 35.2 - - - +
289A VAL* 3.8 14.8 - - + +
325A SER* 3.8 10.5 + - - +
326A LYS* 1.3 76.8 - - - +
328A ASP* 1.3 61.6 + - - +
330A VAL* 3.0 18.0 + - - +
331A ILE* 3.0 19.4 + - + +
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Residues in contact with ASP 328 (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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268A THR* 3.5 17.1 - - + +
269A ARG* 3.8 7.4 + - - -
272A ARG* 3.2 36.1 + - - -
320A LEU* 3.7 19.7 - - - +
321A ILE* 5.6 1.8 - - - -
322A ASP 6.0 0.4 - - - +
323A THR* 2.6 32.1 + - + +
325A SER* 3.1 25.2 + - - +
327A MET* 1.3 77.0 - - - +
329A GLU* 1.3 61.3 + - + +
331A ILE* 3.8 8.7 - - - +
332A TYR* 3.4 15.1 + - - +
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Residues in contact with GLU 329 (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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321A ILE* 3.1 37.8 - - - +
322A ASP* 3.7 14.6 + - - +
325A SER 3.6 8.2 + - - +
326A LYS* 3.1 25.9 + - + +
327A MET 3.1 0.4 - - - -
328A ASP* 1.3 76.6 - - + +
330A VAL* 1.3 59.2 + - + +
332A TYR* 3.1 10.9 + - - +
333A GLU* 2.9 39.5 + - + +
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Residues in contact with VAL 330 (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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286A THR* 3.8 28.7 - - - +
287A GLY* 4.3 7.6 - - - +
289A VAL* 3.7 25.4 - - + -
294A LEU* 4.9 4.0 - - + -
326A LYS* 3.3 15.7 - - + +
327A MET 3.0 6.2 + - - +
329A GLU* 1.3 72.9 - - + +
331A ILE* 1.3 67.6 + - - +
333A GLU* 3.1 11.7 + - + +
334A GLU* 3.0 38.0 + - + +
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Residues in contact with ILE 331 (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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267A ILE* 3.9 4.0 - - + +
268A THR* 3.7 25.1 - - + +
271A ALA* 3.6 36.3 - - + -
272A ARG* 4.3 11.4 - - - -
275A ASN* 6.0 0.2 - - + -
289A VAL* 4.3 16.2 - - + -
294A LEU* 3.7 23.3 - - + -
327A MET* 3.0 28.4 + - + +
328A ASP* 3.8 10.5 - - - +
330A VAL* 1.3 75.8 - - - +
332A TYR* 1.3 62.0 + - - +
334A GLU* 3.5 0.7 + - - +
335A PHE* 3.0 39.7 + - + -
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Residues in contact with TYR 332 (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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175A LEU* 4.2 13.0 - - + +
177A VAL* 3.7 35.3 - - + +
268A THR* 5.4 1.7 + - - +
319A ALA* 3.9 22.9 - - + -
320A LEU 4.8 6.1 - - - +
321A ILE* 3.9 25.8 - - + -
328A ASP 3.4 10.5 + - - +
329A GLU* 3.1 16.2 + - - +
331A ILE* 1.3 77.9 - - - +
333A GLU* 1.3 72.1 + - + +
335A PHE* 3.4 3.8 + - - +
336A LYS* 3.0 63.6 + - + +
344A HIS* 3.8 20.4 + - - -
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Residues in contact with GLU 333 (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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329A GLU* 2.9 29.2 + - + +
330A VAL* 3.1 15.0 + - + +
332A TYR* 1.3 82.8 - - + +
334A GLU* 1.3 67.3 + - - +
336A LYS* 3.4 24.9 - - - +
269B ARG* 5.2 5.9 + - - -
272B ARG* 5.2 5.0 + - - +
324B GLY 3.3 20.0 - - - +
325B SER* 3.4 29.0 + - - -
326B LYS 5.1 0.3 + - - -
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Residues in contact with GLU 334 (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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291A ALA* 5.2 2.4 - - - +
294A LEU* 3.6 37.7 - - + +
298A LYS* 3.3 34.7 + - - -
330A VAL* 3.0 26.6 + - + +
331A ILE 3.8 4.7 - - - +
332A TYR 3.1 0.2 - - - -
333A GLU* 1.3 77.9 - - - +
335A PHE* 1.3 59.9 + - + +
336A LYS 3.1 11.8 + - - +
338A THR* 3.5 13.3 - - - +
269B ARG* 5.2 7.8 + - - +
272B ARG* 2.8 31.2 + - - +
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Residues in contact with PHE 335 (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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175A LEU* 4.3 24.6 - - + +
267A ILE* 3.6 24.9 - - + -
271A ALA* 4.6 0.4 - - + -
294A LEU* 4.2 15.3 - - + -
297A PRO* 3.4 48.5 - - + -
298A LYS* 3.6 25.8 - - + -
301A PHE* 4.0 20.8 - + + -
331A ILE* 3.0 43.1 + - + +
332A TYR* 3.8 3.4 - - - +
334A GLU* 1.3 75.6 - - + +
336A LYS* 1.3 62.4 + - - +
337A GLY 3.1 3.3 + - - -
338A THR* 2.6 28.6 + - - +
339A GLY 4.0 2.8 + - - -
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Residues in contact with LYS 336 (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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175A LEU* 5.0 6.3 - - - -
332A TYR* 3.0 60.9 + - + +
333A GLU* 3.4 20.6 - - - +
334A GLU 3.1 6.7 - - - +
335A PHE* 1.3 74.5 - - - +
337A GLY* 1.3 59.4 + - - +
338A THR* 3.3 3.5 + - - +
342A GLU* 5.9 1.5 + - - +
344A HIS* 5.2 2.6 + - - -
269B ARG* 4.5 5.9 + - - +
323B THR* 3.7 20.4 - - + +
324B GLY* 5.0 8.7 - - - +
325B SER* 6.2 1.6 - - - -
2701B FPD 3.5 51.3 - - + +
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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