Contacts of the helix formed by residues 346 - 352 (chain B) 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 346 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B PRO* 5.0 0.7 - - - -
182B ALA* 4.7 1.2 - - - +
344B HIS* 4.1 1.4 - - - -
345B LEU* 1.3 72.0 - - - +
347B ARG* 1.3 65.5 + - - +
348B LYS* 3.4 4.7 + - - +
349B ILE* 3.3 24.6 + - - +
350B ALA* 3.4 19.1 + - - +
357B ALA* 3.4 18.5 + - - +
359B ASP* 4.3 18.3 - - - +
392B GLU* 3.7 23.0 + - - -
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Residues in contact with ARG 347 (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 PRO* 4.2 29.2 - - + +
180B PRO* 5.2 9.4 - - - +
181B LYS 5.3 1.5 - - - +
182B ALA* 5.5 1.8 - - - -
322B ASP* 3.8 35.3 + - - +
345B LEU 3.8 2.4 + - - -
346B SER* 1.3 73.3 + - - +
348B LYS* 1.3 65.3 + - + +
350B ALA* 3.4 8.5 + - - +
351B GLU* 3.2 38.6 + - + +
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Residues in contact with LYS 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B SER* 3.3 3.2 + - - +
347B ARG* 1.3 78.4 - - + +
349B ILE* 1.3 65.1 + - + +
351B GLU* 3.1 24.6 + - - +
352B LYS* 3.1 14.9 + - - +
392B GLU* 3.3 32.3 + - + +
393B ILE* 4.1 18.8 - - + +
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Residues in contact with ILE 349 (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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346B SER* 3.3 17.7 - - - +
347B ARG 3.4 0.2 - - - -
348B LYS* 1.3 75.0 - - + +
350B ALA* 1.3 62.2 + - - +
351B GLU 3.5 0.3 + - - -
352B LYS 3.7 3.2 + - - +
354B VAL* 3.0 42.3 + - + +
356B PRO 3.7 9.2 - - - +
357B ALA* 3.2 41.3 - - + +
358B ILE 5.7 0.4 - - - +
359B ASP* 5.9 1.1 - - - -
392B GLU* 3.3 46.4 - - + +
393B ILE* 3.5 19.5 - - + +
396B MET* 4.0 17.0 - - + -
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Residues in contact with ALA 350 (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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181B LYS 3.5 24.2 - - - +
182B ALA* 3.6 23.3 - - + +
346B SER 3.4 8.9 + - - +
347B ARG 3.6 9.0 - - - +
348B LYS 3.2 0.2 - - - -
349B ILE* 1.3 78.8 - - - +
351B GLU* 1.3 61.5 + - + +
353B ARG* 3.3 16.7 + - - +
354B VAL 4.2 7.0 - - - -
355B PHE* 4.5 11.0 - - + -
357B ALA* 3.9 2.8 - - + +
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Residues in contact with GLU 351 (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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388A HIS* 3.6 27.1 + - + +
347B ARG* 3.2 27.7 + - + +
348B LYS* 3.1 21.7 + - - +
350B ALA* 1.3 75.0 - - - +
352B LYS* 1.3 58.6 + - - +
353B ARG* 2.8 24.5 + - - +
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Residues in contact with LYS 352 (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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385A LYS* 6.0 5.8 - - - -
348B LYS 3.1 13.5 + - - +
349B ILE 4.1 2.0 - - - +
350B ALA 3.5 0.2 - - - -
351B GLU* 1.3 73.6 - - - +
353B ARG* 1.3 74.2 + - - +
354B VAL* 3.5 22.5 + - + +
393B ILE* 4.2 32.6 - - + +
397B GLU* 3.6 19.2 + - - +
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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