Contacts of the strand formed by residues 297 - 305 (chain A) in PDB entry 5EMV
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 PHE 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A LEU* 4.2 12.3 - - + -
288A LEU* 3.3 35.4 - - + -
289A TYR* 3.5 42.4 - + + -
292A GLY* 4.2 1.6 - - - -
293A PRO 3.2 32.3 - - - -
294A PRO* 3.7 11.5 - - + +
295A HIS 3.3 2.8 - - - +
296A ALA* 1.3 78.6 - - - +
298A PHE* 1.3 69.9 + - - +
420A LEU* 3.6 22.7 - - + -
423A CYS* 3.4 33.2 - - + -
443A ARG* 4.0 1.9 - - - +
444A LEU* 3.1 30.6 + - + +
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Residues in contact with PHE 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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222A GLY 3.8 15.5 - - - -
223A LEU* 3.8 32.1 - - + -
224A GLY 3.4 26.9 - - - -
266A LEU* 4.0 16.8 - - + -
295A HIS 3.7 23.8 - - - -
296A ALA 3.5 8.3 - - - -
297A PHE* 1.3 78.7 - - - +
299A LEU* 1.3 60.5 + - - +
422A LEU* 3.6 21.8 - - + -
423A CYS 2.9 9.6 + - - +
424A THR* 3.3 7.6 - - + +
425A ALA 2.9 23.9 + - - -
441A ILE* 4.4 4.3 - - + -
442A TYR 3.4 16.2 - - - +
443A ARG* 4.4 7.0 - - + -
444A LEU* 3.4 12.0 - - - +
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Residues in contact with LEU 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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269A VAL* 3.9 34.5 - - + -
274A ILE* 4.3 14.6 - - + -
298A PHE* 1.3 73.4 - - - +
300A VAL* 1.3 68.6 + - - +
301A LYS* 4.9 0.7 - - + +
425A ALA* 3.4 29.8 - - + +
427A VAL* 4.2 27.6 - - + -
441A ILE* 3.5 1.7 - - - +
442A TYR* 2.6 56.2 + - + +
444A LEU* 3.7 17.9 - - + +
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Residues in contact with VAL 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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223A LEU* 3.6 31.4 - - + -
254A ILE* 4.3 4.3 - - + -
299A LEU* 1.3 79.4 - - - +
301A LYS* 1.3 68.7 + - - +
302A PHE* 3.8 33.6 + - + -
424A THR* 3.7 10.1 - - + -
425A ALA 2.8 10.1 + - - -
426A TYR* 3.3 17.7 - - + +
427A VAL* 3.0 27.8 + - - +
439A HIS* 4.2 7.9 - - + -
440A HIS 3.6 4.7 - - - +
441A ILE* 4.1 12.6 - - + -
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Residues in contact with LYS 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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299A LEU* 4.2 0.9 - - + -
300A VAL* 1.3 73.2 - - - +
302A PHE* 1.3 64.6 + - - +
303A TRP* 3.4 35.8 - - + -
427A VAL* 3.5 24.9 - - + +
428A PHE 5.1 1.1 - - - -
429A GLU* 2.9 45.3 + - - +
439A HIS* 3.2 6.8 - - - +
440A HIS 3.0 35.1 + - - +
442A TYR* 4.4 15.7 - - + +
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Residues in contact with PHE 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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233A PHE* 4.1 18.2 - + - -
252A VAL* 3.5 33.4 - - + -
253A HIS 4.2 4.7 - - - -
254A ILE* 3.6 31.9 - - + -
300A VAL* 3.8 4.9 + - + -
301A LYS* 1.3 74.6 - - - +
303A TRP* 1.3 59.6 + - - +
304A ALA 3.7 0.2 - - - -
380A P1L 5.8 0.4 - - + -
426A TYR* 3.3 32.5 - + - -
427A VAL 2.8 10.2 + - - -
428A PHE* 3.5 36.2 - + + -
429A GLU 2.7 32.2 + - - +
437A ALA* 6.3 0.2 - - + -
438A GLN 3.6 5.6 - - - -
439A HIS* 3.6 27.1 - + + -
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Residues in contact with TRP 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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252A VAL* 5.0 0.7 - - - -
301A LYS* 3.4 52.0 - - + -
302A PHE* 1.3 72.1 - - - +
304A ALA* 1.3 65.3 + - - +
429A GLU* 3.3 38.9 + - + +
430A VAL 4.1 9.6 - - - -
431A SER* 3.7 18.3 - - - +
437A ALA* 3.3 7.6 - - - +
438A GLN* 2.9 61.1 + - + +
439A HIS 3.9 2.5 - - - -
440A HIS* 3.9 27.1 - + + -
442A TYR* 5.2 2.5 - - - -
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Residues in contact with ALA 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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251A PHE 3.2 13.2 - - - +
252A VAL* 3.9 14.4 - - + -
302A PHE 3.7 1.0 - - - -
303A TRP* 1.3 73.9 - - - +
305A ASP* 1.3 60.6 + - - +
306A LEU* 3.7 16.8 + - + +
380A P1L 3.9 24.7 - - + -
428A PHE* 5.0 1.8 - - + -
429A GLU 2.9 14.9 + - - +
430A VAL* 3.6 5.0 - - + +
431A SER* 2.8 25.5 + - - +
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Residues in contact with ASP 305 (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 HIS* 2.7 40.8 + - - -
250A LEU 3.7 13.8 - - - +
251A PHE* 2.8 21.5 + - - +
303A TRP 3.9 0.6 + - - -
304A ALA* 1.3 72.7 - - - +
306A LEU* 1.3 56.7 + - - +
307A ASN* 3.1 26.9 + - - +
431A SER* 4.5 4.7 - - - +
432A THR 4.8 8.7 - - - +
433A SER* 4.5 8.9 - - - +
436A GLY* 4.4 11.1 - - - -
437A ALA 4.1 15.9 + - - +
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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