Contacts of the strand formed by residues 460 - 464 (chain A) in PDB entry 4EJJ
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 460 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A ILE* 3.9 29.6 - - + -
160A LEU* 3.9 14.8 - - + -
161A ARG* 3.6 44.0 - - + -
324A GLU* 4.5 0.3 - - - +
328A HIS* 3.5 5.2 - - - -
456A VAL 3.0 18.3 + - - +
457A MET* 3.1 23.7 - - - +
459A ASN* 1.3 95.2 - - + +
461A ARG* 1.3 68.4 + - - +
462A LEU* 4.3 2.7 + - + +
491A PHE* 3.5 49.4 - + + -
492A LEU 3.1 13.7 - - - +
493A PRO* 4.5 8.7 - - + -
494A ARG* 3.4 7.1 - - - -
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Residues in contact with ARG 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLU* 3.5 11.4 - - - +
328A HIS* 4.0 11.2 - - + +
460A PHE* 1.3 78.4 - - - +
462A LEU* 1.3 65.1 + - - +
463A LYS* 3.7 1.6 + - + -
491A PHE* 4.0 1.4 - - - -
492A LEU* 2.9 73.2 + - + +
493A PRO 3.5 18.6 + - - -
494A ARG* 3.6 20.1 + - + +
143B ARG* 4.2 12.5 - - - +
147B GLU* 5.4 1.8 + - - -
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Residues in contact with LEU 462 (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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314A PHE* 3.5 36.6 - - + +
317A LEU* 3.9 25.1 - - + -
318A MET* 3.6 23.9 - - + +
324A GLU* 2.8 30.1 + - - +
456A VAL* 4.4 6.1 - - + -
457A MET* 4.3 17.0 - - + -
460A PHE* 4.8 4.0 - - + +
461A ARG* 1.3 75.2 - - - +
463A LYS* 1.3 60.2 + - - +
464A SER 4.0 0.7 + - - -
489A MET* 3.7 9.0 - - + -
490A SER 4.1 2.7 - - - -
491A PHE* 3.7 32.5 - - + -
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Residues in contact with LYS 463 (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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318A MET* 3.7 3.3 - - - -
461A ARG* 3.7 1.9 + - + +
462A LEU* 1.3 71.3 - - - +
464A SER* 1.3 77.3 + - - +
489A MET* 3.7 3.6 - - - +
490A SER* 3.1 55.4 + - - +
492A LEU* 4.1 27.1 - - + -
143B ARG* 4.6 12.3 - - - +
147B GLU* 3.8 37.4 - - - +
150B GLN* 4.3 12.0 + - - +
340B GLN* 4.9 6.4 + - - -
342B LYS* 6.3 3.4 - - - -
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Residues in contact with SER 464 (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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318A MET* 3.5 27.1 + - - +
462A LEU 4.0 1.2 + - - -
463A LYS* 1.3 97.2 + - - +
465A SER* 1.3 64.1 + - - +
466A GLN* 2.9 24.4 + - - +
468A PRO* 4.6 7.4 - - - +
471A ILE* 3.8 23.5 - - - +
488A THR 5.1 0.4 - - - -
489A MET* 4.9 0.9 - - - -
340B GLN* 4.4 3.3 - - - +
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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