Contacts of the strand formed by residues 297 - 304 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B LEU* 4.2 12.3 - - + -
288B LEU* 3.2 36.3 - - + -
289B TYR* 3.4 34.1 - + + -
292B GLY 4.3 1.6 - - - -
293B PRO 3.2 31.6 - - - -
294B PRO* 3.2 14.5 + - + +
295B HIS* 3.3 1.6 - - - +
296B ALA* 1.3 78.8 - - - +
298B PHE* 1.3 71.9 + - - +
420B LEU* 3.4 21.5 - - + -
423B CYS* 3.4 32.3 - - + -
443B ARG* 4.0 2.1 - - - +
444B LEU* 3.1 37.2 + - + +
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Residues in contact with PHE 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ALA* 3.8 15.7 - - + -
222B GLY 3.5 16.2 - - - -
223B LEU* 3.7 26.7 - - + -
224B GLY 3.2 28.0 - - - -
266B LEU* 5.4 1.6 - - + -
295B HIS 3.7 22.2 - - - -
296B ALA 3.6 7.6 - - - -
297B PHE* 1.3 78.6 - - - +
299B LEU* 1.3 60.6 + - - +
300B VAL 4.2 0.2 - - - -
422B LEU* 3.6 22.2 - - + -
423B CYS 2.8 9.5 + - - +
424B THR* 3.4 5.8 - - + -
425B ALA 2.8 25.3 + - - -
441B ILE* 4.3 14.6 - - + -
442B TYR 3.3 16.4 - - - +
443B ARG* 4.1 12.3 - - + -
444B LEU* 3.4 11.5 - - - +
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B VAL* 3.9 35.4 - - + -
274B ILE* 4.3 15.0 - - + -
298B PHE* 1.3 74.8 - - - +
300B VAL* 1.3 66.4 + - - +
301B LYS* 4.9 1.1 - - + +
425B ALA* 3.4 25.1 - - + +
427B VAL* 4.0 34.3 - - + -
441B ILE* 3.6 1.9 - - - +
442B TYR* 2.7 52.5 + - + +
444B LEU* 3.8 18.3 - - + +
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU* 3.7 20.4 - - + -
254B ILE* 4.0 6.3 - - + -
298B PHE* 5.1 0.2 - - + -
299B LEU* 1.3 78.8 - - - +
301B LYS* 1.3 65.7 + - - +
302B PHE* 3.7 38.9 + - + -
424B THR* 3.6 22.0 - - + -
425B ALA 2.7 8.5 + - - -
426B TYR* 3.4 15.9 - - + +
427B VAL* 2.9 28.7 + - - +
439B HIS* 4.5 3.4 - - + -
440B HIS 3.6 6.5 - - - +
441B ILE* 4.3 11.0 - - + -
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Residues in contact with LYS 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU* 4.2 2.3 + - + +
300B VAL* 1.3 73.6 - - - +
302B PHE* 1.3 62.7 + - - +
303B TRP* 3.4 37.3 - - + -
427B VAL* 3.5 24.9 - - + +
428B PHE 4.7 1.3 - - - -
429B GLU* 2.6 50.1 + - - +
439B HIS* 3.2 7.3 - - - +
440B HIS* 3.1 33.3 + - + +
442B TYR* 4.7 15.9 - - + +
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Residues in contact with PHE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B PHE* 4.1 11.2 - + - -
252B VAL* 3.6 38.8 - - + -
253B HIS 4.3 4.5 - - - -
254B ILE* 3.6 33.0 - - + -
300B VAL* 3.7 4.0 - - + -
301B LYS* 1.3 76.7 - - - +
303B TRP* 1.3 65.0 + - - +
304B ALA 3.7 0.4 - - - -
380B P1L 5.6 0.7 - - + -
426B TYR* 3.3 33.4 - + + -
427B VAL 3.0 6.6 + - - -
428B PHE* 3.6 36.6 - + + -
429B GLU* 2.9 27.5 + - - +
438B GLN 3.6 4.5 - - - -
439B HIS* 3.5 27.8 - + + -
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Residues in contact with TRP 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B VAL* 5.1 0.6 - - - +
301B LYS* 3.4 47.3 - - + +
302B PHE* 1.3 73.7 - - - +
304B ALA* 1.3 64.1 + - - +
429B GLU* 3.3 35.5 + - + -
430B VAL 4.1 11.0 - - - -
431B SER* 3.9 16.3 - - - +
437B ALA* 3.3 7.3 - - - +
438B GLN* 2.9 57.1 + - + +
439B HIS 4.1 12.3 - - - -
440B HIS* 4.2 12.6 - - + -
442B TYR* 5.9 0.7 - - - -
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B PHE* 3.3 13.7 - - + +
252B VAL* 4.0 12.8 - - + -
302B PHE 3.7 0.6 - - - -
303B TRP* 1.3 74.4 - - - +
305B ASP* 1.3 61.7 + - - +
306B LEU* 3.5 11.1 + - + +
380B P1L 3.4 36.8 - - + -
428B PHE* 4.8 2.2 - - + -
429B GLU 2.9 10.0 + - - +
430B VAL* 3.7 5.8 - - - +
431B SER* 2.8 24.8 + - - -
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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
------------------------------------------------------------
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