Contacts of the strand formed by residues 457 - 467 (chain I) in PDB entry 4K4I
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 LEU 457 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448I LEU* 3.9 26.7 - - + +
451I LEU* 3.5 31.5 + - + +
452I ARG* 4.2 23.7 - - + +
455I GLY* 4.4 5.9 - - - -
456I PHE* 1.3 81.5 - - + +
458I THR* 1.3 61.3 + - - +
459I ASP 3.5 1.3 + - - +
460I ASP* 4.9 2.2 - - - +
473I TYR* 3.7 39.3 - - + +
476I VAL 3.4 9.4 - - - +
477I CYS* 4.2 0.7 - - + -
489I LEU* 3.9 28.7 - - + -
491I ILE* 5.1 0.2 - - + -
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Residues in contact with THR 458 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455I GLY 4.2 10.1 - - - +
456I PHE 4.0 9.9 - - - +
457I LEU* 1.3 74.6 - - - +
459I ASP* 1.3 82.1 + - - +
476I VAL* 3.0 26.1 + - - +
478I ARG* 4.2 18.8 - - + +
486I HIS* 3.3 24.8 - - + +
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Residues in contact with ASP 459 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375I ILE* 4.2 20.6 - - + +
378I LYS* 3.2 23.2 + - - -
379I HIS* 3.0 27.2 + - - -
457I LEU 3.5 1.6 + - - -
458I THR* 1.3 98.7 + - - +
460I ASP* 1.3 65.6 + - - +
473I TYR* 3.1 7.6 + - - -
476I VAL* 3.1 37.0 + - + +
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Residues in contact with ASP 460 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371I THR* 5.5 2.4 - - - +
375I ILE* 3.3 20.2 - - - +
452I ARG* 2.6 33.0 + - - +
457I LEU* 4.9 2.9 - - - +
459I ASP* 1.3 76.8 + - - +
461I LEU* 1.3 62.6 + - - +
463I SER* 2.4 33.4 + - - +
473I TYR* 3.0 27.8 + - + -
474I LEU 4.1 1.1 - - - -
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Residues in contact with LEU 461 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342I TRP* 3.8 36.6 - - + -
372I GLN* 3.0 50.3 - - - +
375I ILE* 3.7 29.4 - - + -
376I GLY 5.0 0.9 - - - +
383I PHE* 5.3 1.3 - - + -
460I ASP* 1.3 74.8 - - - +
462I VAL* 1.3 62.9 + - - +
463I SER 4.1 0.7 - - - -
474I LEU* 2.9 11.6 + - + +
475I GLY* 4.0 8.5 - - - +
476I VAL* 4.7 4.0 - - + -
488I ARG* 3.5 45.1 - - - +
10J T 4.3 6.8 - - - +
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Residues in contact with VAL 462 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342I TRP* 5.3 2.0 - - + -
372I GLN* 3.6 14.1 - - - +
461I LEU* 1.3 83.1 - - + +
463I SER* 1.3 65.9 + - - +
464I GLN 3.3 13.3 + - - +
465I GLU* 3.4 28.7 - - + +
472I LYS 5.0 0.2 - - - +
473I TYR* 3.6 1.9 - - - -
474I LEU* 2.9 54.3 + - + +
9J C 3.7 32.8 - - + +
10J T 4.8 2.9 - - - +
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Residues in contact with SER 463 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444I PHE* 3.8 2.1 - - - -
448I LEU* 3.8 13.0 - - - +
452I ARG* 4.1 7.0 - - - -
460I ASP* 2.4 39.8 + - - +
461I LEU 4.1 0.4 - - - -
462I VAL* 1.3 74.4 - - - +
464I GLN* 1.3 64.9 + - - +
473I TYR* 3.5 17.3 - - - -
10J T 5.2 4.6 + - - -
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Residues in contact with GLN 464 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441E ARG* 3.1 44.5 + - - +
444I PHE* 3.5 22.6 - - + -
445I SER* 4.9 7.4 + - - -
448I LEU* 5.6 0.2 - - + -
462I VAL* 3.2 3.9 - - - +
463I SER* 1.3 85.4 - - - +
465I GLU* 1.3 66.4 + - - +
466I GLU* 2.6 33.0 + - + +
471I GLN* 3.8 12.5 + - - -
472I LYS 3.6 5.6 - - - -
9J C 3.3 12.8 - - - +
10J T 5.6 0.5 + - - -
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Residues in contact with GLU 465 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462I VAL* 3.4 26.6 - - + +
464I GLN* 1.3 78.1 - - - +
466I GLU* 1.3 64.6 + - - +
467I ASN* 4.2 2.1 + - + +
470I GLN 4.0 0.3 - - - +
471I GLN* 3.4 4.3 - - - +
472I LYS* 2.8 69.1 + - + +
474I LEU* 4.8 5.2 - - - +
8J A 3.2 41.5 - - - +
9J C 3.2 15.6 + - - +
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Residues in contact with GLU 466 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441E ARG* 3.5 33.0 + - - +
442E GLY* 5.2 2.6 + - - -
469E GLN* 3.7 26.2 + - - +
464I GLN* 2.6 33.7 + - + +
465I GLU* 1.3 79.2 - - - +
467I ASN* 1.3 60.3 + - - +
468I GLY 4.0 7.0 - - - +
470I GLN 3.5 4.0 - - - +
471I GLN* 3.5 23.8 - - + +
8J A 3.4 23.7 + - - +
9J C 2.9 8.1 + - - -
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Residues in contact with ASN 467 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465I GLU* 4.2 2.4 + - + -
466I GLU* 1.3 74.0 - - - +
468I GLY* 1.3 67.8 + - - +
470I GLN* 3.0 29.0 + - + +
529I GLU* 3.2 22.2 + - + +
530I HIS* 2.7 38.4 + - + +
6J G 5.5 1.4 - - - +
7J T 3.7 35.7 + - - +
8J A 3.8 13.3 + - - -
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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
------------------------------------------------------------
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