Contacts of the strand formed by residues 298 - 305 (chain H) in PDB entry 2PUQ
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 MET 298 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H ILE* 3.7 23.1 - - + +
156H GLY* 4.2 10.8 - - - +
157H LYS 3.1 26.2 - - - +
158H VAL* 3.6 20.6 - - + +
282H SER* 3.0 7.1 - - - -
283H GLY 2.8 44.6 + - - +
285H GLY 5.5 0.7 - - - +
287H LEU* 3.6 24.5 - - + -
294H ALA* 3.5 21.1 - - + -
296H GLU* 3.4 17.5 - - - +
297H LEU* 1.3 74.2 - - - +
299H VAL* 1.3 59.3 + - - +
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Residues in contact with VAL 299 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153H ILE* 4.3 1.8 - - - -
156H GLY* 3.2 3.3 - - - -
157H LYS* 2.8 54.7 + - + +
158H VAL 4.4 1.6 - - - +
159H CYS* 3.8 31.2 - - + -
160H PRO* 5.4 2.0 - - + -
164H CYS* 4.3 8.5 - - - -
280H LEU* 4.0 34.1 - - + -
281H VAL 3.4 9.4 - - - +
282H SER* 4.1 9.6 - - - -
298H MET* 1.3 76.6 - - - +
300H LEU* 1.3 63.6 + - - +
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Residues in contact with LEU 300 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H ILE* 3.7 12.6 - - + -
154H VAL 3.9 2.0 - - - +
155H GLY 3.8 13.5 - - - +
156H GLY* 4.1 3.1 - - - -
280H LEU* 3.3 6.6 - - - -
281H VAL* 2.7 44.2 + - + +
299H VAL* 1.3 76.8 - - - +
301H ASN* 1.3 65.4 + - - +
302H VAL* 3.7 22.9 + - + -
337H LYS* 3.6 34.1 - - + +
338H ASP 3.2 44.2 - - - +
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Residues in contact with ASN 301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278H PHE* 3.5 29.6 - - + +
279H SER* 2.7 31.2 + - - +
280H LEU* 3.3 16.6 - - + +
300H LEU* 1.3 75.8 - - - +
302H VAL* 1.4 57.8 + - - +
332H TYR* 3.4 23.6 + - - -
337H LYS* 5.3 0.9 + - - -
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Residues in contact with VAL 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277H ARG 3.8 0.2 - - - +
278H PHE* 4.2 3.4 - - - -
279H SER* 2.9 36.5 + - - +
281H VAL* 3.9 21.8 - - + -
300H LEU* 3.7 27.8 - - + -
301H ASN* 1.4 75.5 - - - +
303H PRO* 1.4 62.9 - - - +
304H ARG 4.0 0.2 + - - -
330H ALA* 3.7 16.2 - - + -
331H GLY* 3.4 29.2 - - - +
332H TYR* 4.1 4.0 - - + -
337H LYS 5.5 0.4 - - - +
338H ASP* 5.5 1.8 - - - -
348H HIS* 4.1 5.9 + - + -
377H TYR* 4.3 10.1 - - - +
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Residues in contact with PRO 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277H ARG* 3.1 26.9 - - + +
278H PHE* 4.2 11.9 - - + -
302H VAL* 1.4 91.7 - - + +
304H ARG* 1.3 60.3 - - - +
305H LEU* 3.9 5.1 - - + +
330H ALA* 2.7 27.2 - - - -
331H GLY 3.0 17.4 + - - +
332H TYR* 3.6 31.4 - - + +
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Residues in contact with ARG 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269H SER* 5.3 1.8 + - - -
273H LEU 4.5 1.3 + - - -
274H ALA* 3.9 46.2 + - - +
276H VAL 4.6 8.3 - - - +
277H ARG* 3.0 27.4 + - - +
279H SER* 5.7 0.4 - - - +
302H VAL 4.0 0.4 + - - -
303H PRO* 1.3 75.5 - - - +
305H LEU* 1.3 74.4 + - - +
328H PHE* 3.6 46.7 - - + +
330H ALA* 3.8 7.9 - - + +
348H HIS* 4.6 10.1 - - + +
359H THR* 4.0 28.5 + - - +
379H ARG* 3.3 35.0 - - - +
381H SER* 5.6 0.6 + - - -
45T TRP* 5.5 3.5 + - - -
91T GLU* 5.1 2.0 + - - -
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Residues in contact with LEU 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303H PRO* 3.9 14.6 - - + +
304H ARG* 1.3 88.1 + - - +
306H MET* 1.4 69.4 + - - +
307H THR* 3.7 2.6 + - - -
309H ASP* 4.0 20.6 - - + -
310H CYS* 4.1 9.6 - - - +
313H GLN* 4.2 9.2 - - - +
328H PHE* 4.5 6.4 - - - +
329H CYS* 3.1 31.0 + - + +
330H ALA* 4.0 6.5 - - - -
331H GLY 4.1 3.6 - - - +
374H PHE* 3.7 48.9 - - + -
91T GLU* 4.9 1.2 - - - +
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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