Contacts of the strand formed by residues 350 - 354 (chain A) in PDB entry 4EFO
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 GLN 350 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336A HIS* 2.7 70.0 + - + +
339A VAL* 3.6 18.8 - - - +
340A TYR* 3.4 8.5 - - - +
345A ILE* 2.9 35.0 + - + -
346A ILE 3.5 8.3 - - - +
347A SER* 3.0 20.3 + - - +
348A SER 3.4 2.1 - - - +
349A ASN* 1.3 76.4 - - - +
351A GLU* 1.3 59.7 + - - +
352A LEU* 4.1 5.6 + - + +
381A VAL* 4.1 11.9 - - + -
382A VAL 3.7 4.0 - - - -
384A LEU* 4.9 3.4 - - - +
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Residues in contact with GLU 351 (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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349A ASN 3.5 1.0 + - - -
350A GLN* 1.3 73.7 - - - +
352A LEU* 1.3 71.4 + - - +
353A ILE* 4.1 9.5 + - + +
358A ARG* 3.8 28.4 - - + +
380A PHE 3.6 0.2 - - - +
381A VAL* 3.5 4.7 - - - -
382A VAL* 2.8 59.3 + - + +
384A LEU* 4.0 27.3 - - + +
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Residues in contact with LEU 352 (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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335A PHE* 3.8 22.0 - - + -
336A HIS* 3.7 34.5 - - + +
350A GLN* 4.1 4.7 + - + +
351A GLU* 1.3 79.8 - - - +
353A ILE* 1.3 58.8 + - - +
358A ARG* 3.5 7.8 - - - +
359A LEU* 2.7 52.4 + - + +
361A LEU* 3.9 26.7 - - + +
370A PHE* 5.1 0.2 - - + -
379A ILE* 3.9 15.0 - - + -
380A PHE 3.4 1.3 - - - -
381A VAL* 3.9 28.3 - - + -
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Residues in contact with ILE 353 (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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316A LEU* 5.0 3.4 - - + -
351A GLU* 4.7 11.4 - - + +
352A LEU* 1.3 80.7 - - - +
354A TYR* 1.3 64.3 + - - +
355A GLU 4.3 0.2 - - - -
356A GLY* 4.0 13.7 - - - +
357A ARG 3.4 24.0 - - - +
358A ARG* 4.5 6.5 - - + +
359A LEU* 4.6 1.1 - - - -
379A ILE* 3.5 4.4 - - - -
380A PHE* 2.8 56.9 + - + +
382A VAL* 3.4 35.2 - - + -
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Residues in contact with TYR 354 (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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353A ILE* 1.3 74.8 - - - +
355A GLU* 1.3 99.7 + - + +
356A GLY 3.1 0.4 - - - -
357A ARG* 2.9 23.0 + - - +
359A LEU* 4.3 25.0 - - + +
371A PRO* 3.5 26.2 - - + -
372A LYS* 2.6 34.1 + - - +
373A THR* 4.2 3.8 - - + -
377A ASN* 3.4 26.1 + - - -
378A PRO 4.0 15.0 - - - -
379A ILE* 4.0 13.2 - - + -
380A PHE* 5.4 0.4 - - - -
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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