Contacts of the strand formed by residues 415 - 425 (chain A) in PDB entry 4U7C
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 SER 415 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413A ARG* 3.1 21.4 + - - +
414A LYS* 1.3 81.8 - - - +
416A MET* 1.3 63.2 + - - +
417A SER* 5.3 0.2 + - - -
512A ARG* 3.2 42.4 + - - -
513A ILE 3.3 12.1 - - - -
514A SER* 4.1 3.8 - - - -
516A PHE* 3.6 6.2 - - - -
8D G 3.6 16.5 + - - +
9D A 3.0 14.5 + - - -
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Residues in contact with MET 416 (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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413A ARG* 3.5 38.4 - - - +
415A SER* 1.3 74.6 - - - +
417A SER* 1.3 67.6 + - - +
442A LEU* 3.8 10.0 - - + +
445A ASP* 3.4 39.9 - - + +
446A LEU* 3.6 28.0 - - + -
449A GLU* 3.9 3.6 - - + +
451A LEU* 3.7 17.0 - - + -
512A ARG* 3.4 0.7 - - - +
513A ILE* 2.9 35.3 + - + +
516A PHE* 4.6 1.8 - - + -
8D G 3.3 16.2 - - - +
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Residues in contact with SER 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A MET* 1.3 81.4 - - - +
418A VAL* 1.3 68.7 + - - +
419A GLU* 5.0 8.3 + - - -
442A LEU* 3.8 2.2 - - - -
445A ASP* 5.4 0.3 - - - +
511A VAL 3.3 12.3 - - - -
512A ARG* 3.6 28.5 + - - -
7D T 3.9 29.2 + - - +
8D G 2.9 19.8 + - - -
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Residues in contact with VAL 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A SER* 1.3 80.7 - - - +
419A GLU* 1.3 65.8 + - - +
420A ARG* 3.8 11.0 - - - +
438A LEU* 3.8 26.3 - - + +
441A GLU* 3.4 26.5 - - + +
442A LEU* 3.9 23.3 - - + +
445A ASP* 3.7 22.9 - - - +
509A MET 4.3 0.2 - - - +
510A GLY* 3.2 1.7 - - - -
511A VAL* 2.9 32.5 + - + +
7D T 3.7 11.9 - - - +
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Residues in contact with GLU 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A SER* 5.0 7.8 + - - -
418A VAL* 1.3 81.7 - - - +
420A ARG* 1.3 67.9 + - - +
438A LEU* 4.7 0.9 - - - -
459A LYS* 3.3 36.8 + - + +
508A LEU* 3.8 21.9 - - + +
509A MET 3.3 13.0 - - - +
510A GLY* 3.6 8.2 - - - -
603A PEG 5.7 0.5 - - - +
6D C 3.5 24.7 + - + +
7D T 2.9 47.2 + - - +
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Residues in contact with ARG 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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418A VAL* 3.8 10.9 - - - +
419A GLU* 1.3 75.9 + - - +
421A THR* 1.3 72.9 + - - +
422A PHE* 3.4 17.0 - - + -
434A LEU* 5.2 1.6 - - + -
438A LEU* 4.4 15.8 - - + +
441A GLU* 2.5 44.1 + - - -
508A LEU* 3.2 4.0 - - - -
509A MET 2.9 31.9 + - - +
170B ASN* 5.9 0.2 - - - +
172B ASP* 2.7 41.8 + - - -
6D C 3.9 6.7 - - - +
7D T 5.7 0.8 + - - -
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Residues in contact with THR 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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420A ARG* 1.3 81.4 - - - +
422A PHE* 1.3 70.8 + - - +
461A LYS* 5.5 0.2 + - - -
507A ARG* 3.3 35.2 + - - +
508A LEU* 3.2 14.8 - - - +
170B ASN* 3.5 8.3 - - - +
4D G 4.4 9.0 - - - +
5D VKJ 3.6 18.1 + - - +
6D C 2.6 36.0 + - - -
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Residues in contact with PHE 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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420A ARG* 3.4 26.0 - - + -
421A THR* 1.3 81.4 - - - +
423A SER* 1.3 78.8 + - - +
424A GLU 3.8 0.2 + - - -
425A ILE* 3.5 28.7 - - + -
434A LEU* 3.8 31.2 - - + -
506A LEU* 3.9 17.0 - - + -
507A ARG* 2.9 39.5 + - - +
508A LEU 3.7 18.2 - - - -
509A MET* 3.8 11.7 - - + -
170B ASN* 3.3 20.9 - - + +
172B ASP* 6.1 1.3 - - + -
173B LYS* 3.9 9.0 - - + -
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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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422A PHE* 1.3 86.9 - - - +
424A GLU* 1.3 70.6 + - - +
425A ILE* 3.6 0.7 - - - +
116B GLU* 2.6 28.8 + - - -
119B ASP* 4.7 8.6 - - - +
120B ASN* 5.3 9.0 - - - -
170B ASN* 3.4 11.0 + - - +
173B LYS* 3.1 22.9 + - - -
3D T 6.6 0.4 - - - -
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Residues in contact with GLU 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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48A ARG* 4.5 6.2 + - - -
422A PHE 3.8 0.4 + - - -
423A SER* 1.3 80.1 - - - +
425A ILE* 1.3 60.7 + - - +
426A ASN* 3.1 28.9 + - - +
463A VAL* 3.7 25.7 - - + +
505A ARG* 2.6 47.6 + - + +
506A LEU 3.3 9.6 - - - +
507A ARG* 5.1 1.5 - - - +
119B ASP* 3.2 33.7 + - + +
173B LYS* 3.2 13.3 + - - -
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Residues in contact with ILE 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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422A PHE* 3.5 30.5 - - + -
423A SER 3.6 8.1 - - - +
424A GLU* 1.3 79.2 - - - +
426A ASN* 1.3 63.6 + - - +
427A LYS 4.2 1.1 - - - +
430A GLU* 3.8 29.4 - - + +
431A GLN* 2.9 41.9 + - + +
434A LEU* 3.8 22.9 - - + -
504A LEU 3.1 6.8 - - - +
506A LEU* 3.1 16.7 + - + +
119B ASP* 5.4 1.1 - - - -
173B LYS* 3.6 29.2 - - + +
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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