Contacts of the strand formed by residues 418 - 425 (chain A) in PDB entry 4FOV
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 THR 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416A SER* 4.2 10.8 - - - +
417A LEU* 1.3 81.4 - - - +
419A VAL* 1.3 64.3 + - - +
439A GLN* 2.8 34.5 + - + +
440A VAL 3.3 20.4 - - - +
441A PRO* 4.4 3.6 - - + -
442A MET* 3.4 17.7 - - - +
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Residues in contact with VAL 419 (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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300A ASP* 5.4 2.9 - - + -
418A THR* 1.3 79.2 - - - +
420A GLU* 1.3 66.2 + - - +
439A GLN* 3.1 10.3 - - - +
440A VAL* 2.9 51.5 + - + +
441A PRO 4.4 1.3 - - - +
442A MET* 3.8 22.2 - - + +
446A TYR* 3.9 22.0 - - + -
448A ASP* 3.5 41.5 - - + +
449A SER* 4.3 0.7 - - - +
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Residues in contact with GLU 420 (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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300A ASP 4.5 0.7 - - - +
419A VAL* 1.3 82.6 - - - +
421A GLN* 1.3 66.3 + - - +
422A TYR* 4.1 4.2 - - - -
435A HIS* 3.3 45.4 + - + +
437A GLY* 2.8 35.0 + - - +
438A LYS 3.2 12.8 - - - +
439A GLN* 3.5 18.6 + - - +
448A ASP* 3.8 10.8 + - - +
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Residues in contact with GLN 421 (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 ASN* 3.1 32.9 + - - +
300A ASP 3.3 8.7 - - - +
301A TYR 4.0 1.0 + - - -
302A GLU* 3.4 34.6 - - - +
303A GLU* 6.4 0.2 - - - -
419A VAL 3.9 0.6 + - - -
420A GLU* 1.3 74.6 - - - +
422A TYR* 1.3 63.3 + - - +
435A HIS* 3.3 6.2 - - - -
436A ASN* 2.8 54.9 + - - +
438A LYS* 2.8 38.2 + - + +
440A VAL* 3.9 18.8 - - + +
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Residues in contact with TYR 422 (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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300A ASP* 2.9 16.2 + - + -
301A TYR* 3.3 49.4 - + + +
302A GLU* 2.8 27.5 + - - +
420A GLU 4.1 3.1 - - - -
421A GLN* 1.3 77.7 - - - +
423A SER* 1.3 63.5 + - - +
433A GLU* 3.9 10.1 - - + -
434A ARG* 3.4 29.2 - - - +
435A HIS* 3.1 29.9 + + - -
436A ASN* 3.9 0.4 - - - -
447A LYS* 4.3 22.6 + - + +
448A ASP* 2.7 41.5 + - - -
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Residues in contact with SER 423 (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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301A TYR* 5.1 0.4 - - - -
302A GLU* 2.6 27.2 + - - -
304A GLN* 3.2 11.9 - - - -
422A TYR* 1.3 71.1 + - - +
424A VAL* 1.3 66.0 + - - +
425A ASP* 5.6 0.2 - - - -
432A ARG 3.8 0.5 - - - +
433A GLU* 3.6 2.5 - - - -
434A ARG* 3.0 37.3 + - - +
436A ASN* 2.9 32.6 + - - +
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Residues in contact with VAL 424 (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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301A TYR* 4.0 28.3 - - + -
304A GLN* 2.6 42.8 + - + +
306A VAL* 4.1 19.4 - - + +
308A TRP* 4.2 17.0 - - + -
319A ILE* 4.0 22.9 - - + -
423A SER* 1.3 78.7 - - - +
425A ASP* 1.3 65.5 + - - +
426A PHE* 5.6 0.2 - - + -
431A LEU* 3.8 9.0 - - + -
432A ARG 3.2 7.2 - - - +
433A GLU* 4.1 11.0 - - + -
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Residues in contact with ASP 425 (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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306A VAL* 6.0 2.7 - - - -
424A VAL* 1.3 78.2 - - - +
426A PHE* 1.3 66.5 + - - +
427A ASP* 2.8 37.6 + - - +
430A SER 3.4 0.7 - - - +
431A LEU* 3.6 2.6 - - - -
432A ARG* 2.8 56.0 + - - +
434A ARG* 2.8 38.8 + - - +
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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
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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