Contacts of the strand formed by residues 316 - 321 (chain F) in PDB entry 3EBL
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 VAL 316 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288F SER* 3.4 7.0 - - - -
290F ILE* 4.0 13.0 - - + -
306F ALA* 4.0 12.1 - - + +
309F LEU* 3.6 41.1 - - + -
310F ARG* 3.9 23.3 + - + +
314F HIS* 3.6 8.8 + - + +
315F HIS* 1.3 89.4 + - - +
317F LYS* 1.3 62.5 + - - +
318F VAL* 3.8 26.6 + - + -
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Residues in contact with LYS 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288F SER 2.7 14.0 + - - +
289F LEU* 3.5 18.7 - - + +
290F ILE* 2.8 28.2 + - - +
315F HIS* 5.5 6.7 - - + -
316F VAL* 1.3 72.4 - - - +
318F VAL* 1.3 66.9 + - - +
319F VAL* 4.5 5.3 - - + +
343F GLU* 3.0 38.8 + - - -
347F PHE* 5.6 7.2 - - + -
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Residues in contact with VAL 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290F ILE* 3.3 13.0 - - + +
292F VAL* 4.5 5.6 - - + -
303F LEU* 3.9 15.9 - - + -
306F ALA* 3.5 31.0 - - + -
310F ARG* 5.1 5.6 - - - +
316F VAL* 3.8 13.2 - - + -
317F LYS* 1.3 77.5 + - - +
319F VAL* 1.3 66.0 + - - +
320F GLN* 3.6 32.9 + - + +
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Residues in contact with VAL 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289F LEU* 3.8 26.2 - - + -
290F ILE 2.8 11.8 + - - +
291F ILE* 3.5 10.9 - - + -
292F VAL 3.0 25.2 + - - +
317F LYS* 4.5 4.3 - - + -
318F VAL* 1.3 75.3 - - - +
320F GLN* 1.3 61.5 + - - +
321F CYS* 3.7 14.1 + - - -
339F GLU* 3.6 23.8 - - - +
340F VAL* 4.3 9.6 - - + -
343F GLU* 3.9 36.3 - - + +
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Residues in contact with GLN 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292F VAL* 3.5 9.4 - - + +
303F LEU* 3.8 33.8 - - + +
318F VAL* 3.6 23.1 + - + +
319F VAL* 1.3 72.5 - - - +
321F CYS* 1.3 63.1 + - - +
322F GLU* 3.6 5.9 + - - +
336F HIS* 4.7 1.6 - - - -
339F GLU* 4.2 8.8 - - - +
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Residues in contact with CYS 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F ILE* 4.6 1.6 - - - -
292F VAL 2.7 15.1 + - - +
293F SER* 4.6 0.2 - - - -
294F GLY* 2.8 25.3 + - - -
319F VAL* 4.1 15.0 - - - -
320F GLN* 1.3 75.2 - - - +
322F GLU* 1.3 60.1 + - - +
323F ASN 3.0 5.0 + - - -
324F ALA* 3.1 16.8 + - + +
328F PHE* 4.0 8.5 - - + -
336F HIS* 3.4 34.8 - - + +
339F GLU* 4.4 2.9 - - - -
340F VAL* 3.7 30.1 - - - -
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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