Contacts of the helix formed by residues 474 - 485 (chain I) in PDB entry 2VKZ
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 474 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449I SER* 6.1 0.9 - - - -
450I PHE 5.8 0.5 + - - -
471I LEU* 4.1 3.1 - - - +
473I GLY* 1.3 72.1 - - - -
475I ILE* 1.3 65.8 + - - +
476I SER* 3.5 9.9 + - - -
477I GLU* 3.3 43.7 + - - +
478I ARG* 3.2 20.1 + - - +
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Residues in contact with ILE 475 (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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281I VAL* 4.4 8.7 - - + -
450I PHE* 3.4 35.3 + - + +
451I ASN 4.3 0.4 - - - -
452I ALA* 3.7 31.4 - - + +
455I ILE* 4.6 8.5 - - + -
468I LEU* 3.5 48.2 - - + +
469I ARG* 4.3 0.9 - - - -
471I LEU* 4.1 11.4 - - + +
473I GLY 4.6 4.9 - - - +
474I SER* 1.3 70.9 + - - +
476I SER* 1.3 68.2 + - - +
478I ARG* 3.3 1.9 + - - +
479I ILE* 3.2 29.0 + - + +
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Residues in contact with SER 476 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302I VAL* 6.3 0.2 - - - -
440I ASN* 3.5 5.5 + - - -
443I LEU* 3.5 27.2 - - - +
448I VAL* 5.2 2.6 + - - -
449I SER* 4.6 8.5 - - - -
450I PHE* 4.2 36.0 + - - +
474I SER* 3.5 9.4 + - - -
475I ILE* 1.3 80.0 - - - +
477I GLU* 1.3 65.5 + - - +
478I ARG 3.0 1.4 + - - -
479I ILE* 3.1 16.7 + - - +
480I VAL* 3.1 13.7 + - - +
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Residues in contact with GLU 477 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440I ASN* 3.3 42.3 - - - +
474I SER* 3.3 30.6 + - - +
475I ILE 3.4 0.2 - - - -
476I SER* 1.3 81.8 + - - +
478I ARG* 1.3 60.3 + - - +
480I VAL* 3.6 2.6 - - - +
481I ASP* 3.1 23.7 + - - +
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Residues in contact with ARG 478 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461I ASP* 2.6 52.0 + - - +
463I PHE* 4.3 6.5 - - - +
464I ASP* 3.8 18.5 + - - -
468I LEU* 4.1 5.4 - - + -
471I LEU* 3.7 26.5 - - + -
474I SER 3.2 14.4 + - - +
475I ILE 3.4 9.0 - - - +
476I SER 3.0 1.0 + - - -
477I GLU* 1.3 75.5 - - - +
479I ILE* 1.3 58.6 + - - +
481I ASP* 3.0 9.7 + - - +
482I CYS* 2.8 37.1 + - - +
486I LEU* 3.5 28.1 - - - +
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Residues in contact with ILE 479 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277I LEU* 3.4 32.8 - - + -
278I VAL* 4.2 23.3 - - + -
281I VAL* 4.1 27.6 - - + -
302I VAL* 5.6 3.4 - - + -
306I ILE* 6.4 0.2 - - + -
450I PHE* 4.4 15.0 - - + -
468I LEU* 3.7 21.1 - - + -
475I ILE* 3.2 16.2 - - + +
476I SER* 3.1 10.1 + - - +
478I ARG* 1.3 74.8 - - - +
480I VAL* 1.3 63.9 + - + +
482I CYS* 3.6 9.3 - - - +
483I ILE* 3.4 30.9 + - - +
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Residues in contact with VAL 480 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302I VAL* 5.3 4.5 - - + -
306I ILE* 5.2 12.1 - - + -
436I SER* 4.3 13.5 - - - +
439I ILE* 4.0 16.2 - - + -
440I ASN* 3.7 20.4 - - - +
443I LEU* 3.7 27.6 - - + -
476I SER 3.1 15.3 + - - +
477I GLU 3.6 8.3 - - - +
478I ARG 3.1 0.2 - - - -
479I ILE* 1.3 77.5 - - + +
481I ASP* 1.3 59.9 + - - +
482I CYS 3.0 3.6 - - - -
483I ILE* 3.4 3.0 + - - +
484I ILE* 3.0 52.5 + - + +
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Residues in contact with ASP 481 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436I SER* 3.9 16.8 + - - +
440I ASN* 6.1 0.2 - - - +
477I GLU 3.1 12.9 + - - +
478I ARG* 3.0 9.7 + - - +
480I VAL* 1.3 79.9 - - + +
482I CYS* 1.3 57.1 + - - +
483I ILE 3.3 0.4 - - - -
484I ILE* 4.0 4.0 - - - +
485I ARG* 2.4 51.9 + - - +
486I LEU* 3.1 33.2 + - + +
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Residues in contact with CYS 482 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274I SER* 5.6 0.2 - - - -
277I LEU* 4.0 9.2 - - + -
428I HIS* 3.6 7.4 + - - -
461I ASP* 3.8 19.3 - - - -
462I THR* 3.6 45.4 + - - +
463I PHE* 4.2 2.2 - - - -
468I LEU* 6.0 0.2 - - - -
478I ARG* 2.8 29.0 + - - +
479I ILE* 3.6 13.9 - - - +
480I VAL 3.0 0.4 - - - -
481I ASP* 1.3 78.9 - - - +
483I ILE* 1.3 60.8 + - - +
486I LEU* 3.4 27.5 - - - +
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Residues in contact with ILE 483 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274I SER* 3.1 30.3 - - - +
275I GLN* 3.5 18.6 - - - +
277I LEU* 4.5 9.0 - - + -
278I VAL* 3.7 24.7 - - + -
306I ILE* 4.1 20.6 - - + -
427I PHE* 3.9 25.5 - - + -
428I HIS* 3.3 32.1 + - - -
479I ILE 3.4 18.1 + - - +
480I VAL 3.9 2.5 - - - +
482I CYS* 1.3 83.9 - - - +
484I ILE* 1.3 64.6 + - + +
485I ARG 3.7 0.4 - - - -
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Residues in contact with ILE 484 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306I ILE* 4.7 5.6 - - + -
310I CYS* 3.5 21.3 - - - -
428I HIS* 3.4 5.2 + - - +
429I SER 3.3 23.7 + - - +
432I LEU* 3.7 36.6 - - + +
433I VAL* 4.3 3.8 - - - +
435I ALA 4.8 0.7 - - - +
436I SER* 4.5 15.9 - - - +
439I ILE* 3.3 33.4 - - + -
480I VAL* 3.0 31.6 + - + +
481I ASP* 4.7 0.4 - - - +
483I ILE* 1.3 90.9 - - + +
485I ARG* 1.3 62.2 + - + +
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Residues in contact with ARG 485 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367I GLU* 4.5 5.5 - - - +
428I HIS* 3.7 15.3 - - - +
429I SER* 4.2 6.5 + - - +
430I HIS* 6.1 0.2 - - - -
433I VAL* 3.9 33.0 - - + -
436I SER* 6.1 0.7 - - - -
481I ASP* 2.4 54.1 + - - +
484I ILE* 1.3 84.3 - - + +
486I LEU* 1.3 97.6 + - + +
487I PRO* 3.9 3.8 - - - +
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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