Contacts of the strand formed by residues 486 - 493 (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 HIS 486 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379I HIS* 3.4 33.0 + + - +
382I ASP* 2.9 38.5 + - - +
383I PHE* 3.6 9.6 - - + -
458I THR* 3.3 37.8 - - + +
459I ASP* 5.2 0.2 + - - -
476I VAL* 3.7 12.6 - - + -
477I CYS 3.4 4.9 - - - -
478I ARG* 3.5 40.7 + - + -
484I ARG 5.1 0.6 + - - -
485I ARG* 1.3 72.2 - - - +
487I ARG* 1.3 67.7 + - - +
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Residues in contact with ARG 487 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382I ASP 3.3 23.1 + - - -
383I PHE* 3.8 7.6 - - - -
385I GLU* 3.3 43.5 + - - -
387I MET* 3.6 41.1 - - + +
388I PRO* 4.2 2.0 - - - +
391I GLU* 2.8 43.0 + - - +
395I ILE* 4.0 17.5 - - + -
426I GLY 5.9 0.4 - - - -
476I VAL* 3.3 4.0 - - - -
477I CYS* 2.8 36.5 + - - +
478I ARG* 5.9 0.2 - - - -
485I ARG* 3.9 23.5 - - - +
486I HIS* 1.3 80.6 - - - +
488I ARG* 1.3 63.7 + - - +
489I LEU 3.6 0.2 + - - -
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Residues in contact with ARG 488 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342I TRP* 3.1 34.8 - - + +
383I PHE* 3.8 37.5 - - + -
426I GLY 5.1 3.2 + - - +
427I ASP* 3.6 26.1 + - + +
428I VAL* 3.1 23.7 + - - +
461I LEU* 3.5 24.0 - - - +
474I LEU* 4.1 3.4 - - - +
475I GLY 2.8 37.9 + - - +
477I CYS* 5.3 0.3 - - - -
487I ARG* 1.3 77.1 - - - +
489I LEU* 1.3 62.5 + - - +
490I ASP* 2.9 34.3 + - - -
6K C 2.9 27.1 + - - -
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Residues in contact with LEU 489 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395I ILE* 4.0 18.6 - - + -
399I VAL* 4.2 2.2 - - + -
428I VAL* 3.3 10.1 - - + +
430I VAL* 4.1 14.8 - - + -
456I PHE* 3.7 30.3 - - + -
457I LEU* 3.9 14.1 - - + -
473I TYR* 3.9 3.5 - - + -
474I LEU 3.7 0.3 - - - -
475I GLY* 2.8 40.1 + - - +
476I VAL 4.9 0.4 - - - +
477I CYS* 4.0 18.4 - - + -
487I ARG 3.6 0.4 + - - -
488I ARG* 1.3 74.7 - - - +
490I ASP* 1.3 82.8 + - - +
491I ILE* 3.8 24.7 - - + -
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Residues in contact with ASP 490 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427I ASP* 5.9 0.2 - - - -
428I VAL 2.8 7.3 + - - -
429I ASP* 3.7 28.5 + - + +
430I VAL 2.9 25.1 + - - -
473I TYR 3.2 7.0 - - - +
474I LEU* 3.1 25.0 - - + +
488I ARG* 2.9 38.3 + - - -
489I LEU* 1.3 76.1 - - - +
491I ILE* 1.3 69.4 + - - +
492I ILE* 4.4 9.4 - - + -
603I CA 4.2 1.2 - - - -
6K C 3.6 20.4 - - - +
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Residues in contact with ILE 491 (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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399I VAL* 4.2 8.5 - - + -
430I VAL* 3.4 11.9 - - + +
432I ILE* 4.0 25.4 - - + -
444I PHE* 4.0 7.3 - - + -
447I LEU* 4.3 9.9 - - + -
448I LEU* 4.3 13.5 - - + -
451I LEU* 3.8 29.8 - - + -
457I LEU* 5.1 0.7 - - + -
471I GLN 3.7 0.9 - - - +
472I LYS* 3.3 2.6 - - - -
473I TYR* 2.9 45.1 + - + +
489I LEU* 3.8 24.7 - - + -
490I ASP* 1.3 79.9 - - - +
492I ILE* 1.3 63.6 + - - +
493I VAL* 4.7 7.2 - - + -
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Residues in contact with ILE 492 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429I ASP* 4.4 10.8 - - + -
430I VAL 3.0 17.8 + - - +
431I LEU* 3.5 10.1 - - + +
432I ILE* 3.0 27.3 + - - +
470I GLN* 4.2 10.3 - - + +
471I GLN 3.2 10.1 - - - +
472I LYS* 3.9 22.9 - - + -
490I ASP* 4.4 16.4 - - + +
491I ILE* 1.3 78.6 - - - +
493I VAL* 1.3 64.0 + - - +
494I VAL* 3.6 21.5 - - + -
506I PHE* 4.1 44.9 - - + -
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Residues in contact with VAL 493 (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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432I ILE* 3.4 31.4 - - + +
440I HIS* 3.6 39.5 - - + +
443I ILE* 4.9 5.2 - - + -
444I PHE* 3.8 30.3 - - + +
447I LEU* 5.2 3.4 - - + -
469I GLN 4.0 2.3 - - - +
470I GLN* 3.3 2.4 - - - -
471I GLN* 2.9 48.2 + - - +
491I ILE* 4.7 4.3 - - + -
492I ILE* 1.3 74.3 - - - +
494I VAL* 1.3 66.9 + - - +
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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
------------------------------------------------------------
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