Contacts of the strand formed by residues 295 - 304 (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 ASN 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A TYR 3.4 2.9 - - - -
236A LYS* 3.6 12.8 - - - +
238A GLY* 2.9 29.8 + - - +
239A ASN 2.9 23.2 + - - -
240A GLU* 4.9 0.8 - - - +
241A GLY 4.7 1.4 - - - +
242A ASP* 2.9 34.2 + - + +
243A ALA 4.5 2.8 - - - +
244A PRO* 3.4 8.4 - - + +
245A ILE* 3.0 19.2 + - - +
294A VAL* 1.3 75.6 - - - +
296A VAL* 1.3 66.0 + - - +
481A ASN* 5.0 0.8 - - - +
513A SO4 3.9 22.3 + - - +
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Residues in contact with VAL 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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233A MSE 3.7 0.5 - - - +
235A TYR* 2.7 43.5 + - + +
245A ILE* 3.3 15.5 - - + +
247A LEU* 4.4 8.5 - - + -
284A MSE 3.7 28.0 - - + -
287A ILE* 4.0 17.3 - - + -
294A VAL* 3.6 28.7 - - + +
295A ASN* 1.3 81.3 - - - +
297A VAL* 1.3 67.6 + - - +
298A GLY 4.1 0.2 - - - -
474A LEU* 4.2 18.2 - - + -
513A SO4 4.1 1.2 + - - -
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Residues in contact with VAL 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A CYS* 4.1 2.5 - - + -
233A MSE 3.4 14.1 - - - +
234A GLU* 4.1 4.7 - - + -
244A PRO* 3.8 22.2 - - + -
245A ILE 2.9 6.7 + - - +
246A VAL* 3.4 12.9 - - + +
247A LEU 2.9 26.0 + - - +
296A VAL* 1.3 81.1 - - - +
298A GLY* 1.3 64.7 + - - +
299A VAL* 3.7 20.0 - - + -
349A TYR* 4.0 36.1 - - + +
513A SO4 3.9 14.8 - - - +
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Residues in contact with GLY 298 (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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231A VAL 3.6 1.0 - - - +
232A CYS* 3.4 1.7 - - - -
233A MSE 2.7 45.8 + - - +
247A LEU* 3.7 5.4 - - - -
280A VAL* 3.7 20.6 - - - -
284A MSE 3.7 19.5 - - - -
297A VAL* 1.3 71.4 - - - +
299A VAL* 1.3 59.4 + - - +
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Residues in contact with VAL 299 (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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230A THR* 4.2 11.7 - - + -
231A VAL 3.2 7.2 - - - +
232A CYS* 4.1 11.0 - - - -
246A VAL* 3.8 10.8 - - + -
247A LEU 2.9 10.9 + - - +
248A VAL* 4.4 4.3 - - + -
249A GLY* 2.9 25.8 + - - -
280A VAL* 4.2 3.2 - - - +
297A VAL* 3.7 19.7 - - + -
298A GLY* 1.3 78.9 - - - +
300A MSE 1.3 69.1 + - - +
342A THR* 3.7 28.7 - - + -
346A ILE* 3.8 26.0 - - + -
349A TYR* 4.7 0.7 - - + -
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Residues in contact with MSE 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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185A MSE 3.8 34.3 - - + +
189A ALA* 4.1 8.3 - - + -
229A TYR 3.5 1.7 - - - +
230A THR* 3.3 5.4 - - - +
231A VAL* 2.8 63.7 + - + +
233A MSE 3.8 13.2 - - + -
249A GLY 3.7 3.4 - - - -
277A VAL* 3.6 34.5 - - + +
280A VAL* 4.6 5.8 - - + -
281A MSE 3.6 25.8 - - - +
299A VAL* 1.3 82.6 - - - +
301A GLY* 1.3 60.3 + - - +
302A LEU* 3.7 16.2 + - + +
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Residues in contact with GLY 301 (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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229A TYR 3.8 3.6 - - - -
230A THR* 4.8 3.1 - - - -
249A GLY 3.1 12.7 + - - -
250A LYS 4.1 0.2 - - - -
251A GLY* 3.0 28.9 + - - +
299A VAL 4.3 0.4 - - - -
300A MSE 1.3 70.3 - - - +
302A LEU* 1.3 62.2 + - - -
338A VAL* 4.0 23.6 - - - +
342A THR* 4.2 16.0 - - - +
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Residues in contact with LEU 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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182A THR* 3.8 26.5 - - + +
185A MSE 3.8 37.2 - - + -
186A LEU 4.4 2.0 - - - +
209A MSE 5.8 0.2 - - - +
228A ASN* 3.2 7.8 + - - +
229A TYR* 2.9 43.5 + - + +
231A VAL* 3.8 25.1 - - + -
251A GLY 3.6 9.6 - - - +
274A MSE 4.3 4.7 - - + -
277A VAL* 4.2 18.8 - - + -
300A MSE 4.2 13.0 - - + +
301A GLY* 1.3 80.0 - - - +
303A ALA* 1.3 65.1 + - - +
338A VAL* 4.8 1.0 - - - +
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Residues in contact with ALA 303 (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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182A THR* 3.6 11.0 - - - +
220A VAL* 4.4 11.4 - - + -
221A GLY 4.5 1.3 - - - +
227A SER 4.8 0.4 - - - -
228A ASN* 3.4 29.6 - - - +
251A GLY 3.4 6.6 + - - +
252A LEU* 3.4 5.0 - - + +
253A VAL* 2.8 34.5 + - - +
301A GLY 4.2 0.2 + - - -
302A LEU* 1.3 78.0 - - - +
304A GLU* 1.3 54.7 + - - +
338A VAL* 4.4 19.5 - - + +
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Residues in contact with GLU 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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182A THR* 4.5 1.0 - - - +
220A VAL 3.2 16.5 - - - +
221A GLY* 3.4 6.9 - - - -
224A SER* 3.0 36.8 + - - +
225A TYR* 3.9 2.4 + - - +
226A MSE 3.3 57.6 + - + +
252A LEU* 3.8 3.6 - - - -
253A VAL* 3.9 15.0 - - + +
254A PHE* 5.1 7.4 - - + +
303A ALA* 1.3 75.6 - - - +
305A ASN* 1.3 70.5 + - - +
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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