Contacts of the strand formed by residues 327 - 335 (chain A) in PDB entry 5E2Q
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 GLU 327 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A VAL* 3.4 20.5 - - + +
51A GLN* 3.6 13.2 - - + +
52A THR* 4.7 1.2 + - - -
171A TYR* 3.2 20.3 + - - +
314A PHE* 4.1 1.1 - - - -
315A ILE 3.4 17.3 + - - -
316A GLU* 3.0 17.3 + - + +
318A TYR 6.2 0.2 - - - +
319A ARG* 3.1 41.4 + - + +
325A ARG 4.1 0.6 + - - -
326A GLY* 1.3 72.1 - - - -
328A PHE* 1.3 75.1 + - - +
329A GLU* 3.5 6.9 + - - +
384A SER* 2.7 27.4 + - - -
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Residues in contact with PHE 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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41A ALA 4.5 3.1 - - - -
44A GLY* 3.2 46.2 - - - +
45A GLY* 4.0 2.9 - - - -
47A ALA* 4.4 5.4 - - + -
48A VAL* 3.2 22.1 - - + +
51A GLN* 3.0 19.1 + - - +
255A LEU* 3.9 24.0 - - + -
258A VAL* 4.6 4.0 - - + -
285A PHE* 4.3 7.2 - + - -
312A ILE* 3.7 30.1 - - + -
313A GLY* 3.4 17.5 - - - -
314A PHE* 3.5 37.2 - + + -
327A GLU* 1.3 76.8 - - - +
329A GLU* 1.3 88.4 + - - +
383A GLY* 4.1 3.8 - - - -
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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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311A TYR* 5.8 1.7 - - - +
312A ILE* 3.5 4.3 - - - +
313A GLY 2.9 30.7 + - - +
315A ILE* 3.6 31.6 - - + +
316A GLU* 3.5 20.1 + - - +
327A GLU* 4.4 5.0 - - + +
328A PHE* 1.3 85.1 - - - +
330A GLY* 1.3 60.2 + - - +
331A PHE* 4.8 6.1 - - + -
381A PHE* 4.0 16.1 - - + -
382A ALA* 3.9 17.3 - - - +
383A GLY* 4.7 2.7 - - - -
390A ILE* 4.7 8.1 - - - +
392A ILE* 6.1 0.5 - - - +
2B ARG* 3.0 29.2 + - - +
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Residues in contact with GLY 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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41A ALA* 3.7 16.5 - - - +
311A TYR 3.2 13.7 - - - -
312A ILE* 3.9 10.8 - - - -
329A GLU* 1.3 81.3 - - - +
331A PHE* 1.3 62.8 + - - +
381A PHE* 3.7 1.9 - - - -
382A ALA* 3.0 31.8 + - - +
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Residues in contact with PHE 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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41A ALA* 5.1 0.4 - - - -
300A TRP* 4.9 1.8 - + - -
309A GLU* 4.2 9.9 - - + -
310A SER* 3.3 42.6 - - - -
311A TYR* 3.0 42.6 + + + +
329A GLU* 4.8 6.1 - - - -
330A GLY* 1.3 74.2 - - - -
332A VAL* 1.3 69.7 + - - +
333A ALA* 4.6 2.5 - - + -
376A LEU* 3.9 27.6 - - + -
378A VAL* 5.3 0.7 - - + -
380A THR 3.1 12.8 - - - +
381A PHE* 3.4 38.8 - + + -
390A ILE* 3.9 18.8 - - + -
392A ILE* 3.9 14.6 - - + -
407A VAL* 4.8 5.2 - - + -
409A LEU* 5.6 2.7 - - + -
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Residues in contact with VAL 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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34A ALA* 3.8 23.8 - - + -
37A LEU* 3.6 31.6 - - + +
38A SER* 3.6 26.9 - - - +
41A ALA* 5.1 1.6 - - + -
308A VAL* 3.7 24.0 - - + -
309A GLU 3.7 3.1 - - - +
310A SER* 4.6 2.5 - - - -
331A PHE* 1.3 79.7 - - - +
333A ALA* 1.3 65.2 + - - +
378A VAL* 3.9 0.5 - - - -
379A LEU* 2.9 29.4 + - + +
380A THR* 2.8 20.1 + - + +
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Residues in contact with ALA 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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308A VAL* 3.3 7.8 - - - +
309A GLU 2.9 33.2 + - - +
331A PHE* 4.6 5.2 - - + -
332A VAL* 1.3 78.2 - - - +
334A VAL* 1.3 64.6 + - - +
376A LEU* 3.6 35.0 - - + -
377A ASP 3.3 18.2 - - - +
378A VAL* 3.8 7.6 - - + -
379A LEU* 4.1 2.5 - - - +
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Residues in contact with VAL 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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22A ALA* 3.6 47.3 - - + +
25A LEU* 5.8 3.8 - - + -
26A LEU* 3.8 23.8 - - + -
307A ILE* 3.5 12.6 - - + +
308A VAL* 4.9 1.6 - - + -
333A ALA* 1.3 74.1 - - - +
335A VAL* 1.3 73.3 + - - +
336A ASN* 3.1 1.6 + - - -
376A LEU* 4.6 1.1 - - - -
377A ASP* 2.9 32.6 + - - +
379A LEU* 3.8 27.1 - - + -
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Residues in contact with VAL 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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305A GLY* 5.5 0.9 - - - -
306A PRO* 3.2 36.8 - - + +
307A ILE* 3.0 17.1 + - - +
309A GLU* 4.2 15.9 - - + -
334A VAL* 1.3 75.4 - - - +
336A ASN* 1.3 60.3 + - - +
337A LYS* 3.1 31.4 + - + +
340A SER* 3.8 10.3 - - - +
344A GLU* 6.0 0.2 - - - +
374A THR* 3.8 27.6 - - + +
375A SER 3.8 4.3 - - - -
376A LEU* 4.1 16.4 - - + -
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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