Contacts of the strand formed by residues 245 - 253 (chain A) in PDB entry 3PEI
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 ILE 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A ALA 3.9 0.4 + - - +
244A PRO* 1.3 72.1 - - - +
246A VAL* 1.3 61.3 - - - +
247A LEU* 4.3 14.1 - - + -
294A VAL* 4.4 9.9 - - + -
295A ASN 3.0 11.2 + - - +
296A VAL* 3.3 7.9 - - + +
297A VAL 2.9 23.6 + - - -
352A LYS* 3.8 22.7 - - + +
353A ALA* 3.6 9.9 - - + +
355A ILE* 4.6 3.8 - - + -
473A TYR* 3.8 26.9 - - + +
474A LEU* 3.9 22.4 - - + -
477A GLN* 3.7 41.1 - - + +
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Residues in contact with VAL 246 (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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244A PRO* 4.3 3.8 - - + +
245A ILE* 1.3 77.0 - - - +
247A LEU* 1.3 64.2 + - - +
248A VAL* 3.8 17.4 + - + -
297A VAL* 3.4 12.3 - - + +
299A VAL* 3.8 27.8 - - + -
346A ILE* 4.1 12.8 - - + -
349A TYR* 4.3 18.6 - - + -
351A PRO* 3.4 28.3 - - + -
353A ALA 2.9 11.9 + - - +
354A VAL* 3.3 7.6 - - + +
355A ILE 3.0 25.3 + - - +
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Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ILE* 4.3 8.1 - - + -
246A VAL* 1.3 75.3 - - - +
248A VAL* 1.3 62.0 + - - +
280A VAL* 4.4 18.8 - - + +
283A THR* 3.7 20.9 - - + -
284A MSE 3.3 31.9 - - + -
296A VAL* 4.4 7.2 - - + -
297A VAL 2.9 9.3 + - - +
298A GLY* 3.7 0.4 - - - -
299A VAL* 2.9 28.8 + - - +
355A ILE* 3.3 35.9 - - + +
357A LEU* 5.6 3.1 - - + -
470A LEU* 4.4 18.4 - - + -
474A LEU* 4.5 10.8 - - + -
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Residues in contact with VAL 248 (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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246A VAL* 3.8 19.7 - - + -
247A LEU* 1.3 75.5 - - - +
249A GLY* 1.3 63.6 + - - +
280A VAL* 4.3 2.2 - - - -
299A VAL* 3.6 8.7 - - + +
339A LEU* 3.7 22.8 - - + +
342A THR* 3.7 25.4 - - + -
343A LEU* 4.1 20.0 - - + -
346A ILE* 4.3 9.2 - - + -
354A VAL* 4.1 8.5 - - + -
355A ILE 2.8 10.1 + - - -
356A ASP* 3.1 11.2 - - + +
357A LEU* 2.8 29.7 + - - +
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Residues in contact with GLY 249 (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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248A VAL* 1.3 80.4 - - - +
250A LYS* 1.3 61.0 + - - -
276A GLY 3.9 6.7 - - - -
277A VAL* 3.5 7.4 - - - +
280A VAL* 3.8 16.7 - - - +
299A VAL 2.9 13.2 + - - -
300A MSE 3.7 0.2 - - - -
301A GLY* 3.1 26.3 + - - -
339A LEU* 4.6 2.0 - - - +
357A LEU 3.7 5.6 - - - -
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Residues in contact with LYS 250 (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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249A GLY* 1.3 72.0 - - - -
251A GLY* 1.3 60.0 - - - +
252A LEU* 4.1 11.9 + - + +
255A ASP* 2.6 36.5 + - - +
272A MSE 4.2 0.6 + - - -
273A ASP 4.1 8.7 + - - +
274A MSE 4.5 2.6 - - - +
276A GLY* 3.7 9.5 + - - -
277A VAL* 3.5 13.5 + - - +
301A GLY* 4.3 2.2 - - - -
335A GLY* 3.9 23.6 - - - +
338A VAL* 5.7 5.4 - - + -
339A LEU* 3.8 25.8 - - + +
357A LEU 3.3 11.6 + - - +
358A ALA* 3.7 23.6 - - + -
359A THR* 3.4 29.5 + - - +
360A LEU* 4.2 10.3 - - + -
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Residues in contact with GLY 251 (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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250A LYS* 1.3 73.6 - - - +
252A LEU* 1.3 61.6 + - - +
253A VAL* 3.5 2.6 + - - +
274A MSE 3.7 24.7 - - - +
277A VAL* 3.6 16.2 - - - +
301A GLY 3.0 20.1 + - - +
302A LEU* 3.6 4.1 - - - +
303A ALA 3.4 19.4 + - - +
338A VAL* 5.6 0.8 - - - +
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Residues in contact with LEU 252 (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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220A VAL* 4.0 16.2 - - + -
250A LYS* 3.8 13.6 - - + +
251A GLY* 1.3 72.8 - - - +
253A VAL* 1.3 67.1 + - - +
254A PHE 3.5 1.7 + - - -
255A ASP* 3.5 44.0 + - + +
272A MSE 4.3 4.7 - - - +
273A ASP 4.8 1.6 + - - +
274A MSE 3.8 8.0 - - - +
303A ALA* 3.4 20.6 - - + +
304A GLU 3.8 2.0 - - - -
305A ASN* 2.4 48.9 - - - +
334A GLU* 4.2 4.9 - - + -
335A GLY* 3.8 24.0 - - - +
338A VAL* 4.6 8.5 - - + -
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Residues in contact with VAL 253 (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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177A ALA* 3.6 29.4 - - + +
180A CYS 3.7 22.4 - - - +
182A THR* 4.2 11.2 - - + +
226A MSE 4.1 21.8 - - + -
251A GLY 3.5 0.4 + - - +
252A LEU* 1.3 71.0 - - - +
254A PHE* 1.3 74.9 + - + +
274A MSE 4.0 22.9 - - + -
303A ALA 2.8 20.4 + - - +
304A GLU* 4.2 9.6 - - + -
305A ASN* 3.1 21.3 + - - +
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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