Contacts of the helix formed by residues 415 - 420 (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 CYS 415 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413I VAL* 3.6 29.6 - - - -
414I ALA* 1.3 72.4 - - - +
416I GLY* 1.3 72.5 + - - +
418I TYR* 3.4 9.4 + - - +
419I ARG* 3.2 19.0 + - - -
428I VAL* 6.1 0.2 - - - -
429I ASP* 2.8 21.8 + - + +
431I LEU* 3.9 18.6 - - - -
503I LEU* 4.0 13.7 - - - -
506I PHE* 3.4 26.5 - - + +
507I THR* 4.0 8.1 - - - +
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Residues in contact with GLY 416 (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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415I CYS* 1.3 84.8 - - - +
417I SER* 1.3 57.6 + - - -
419I ARG* 3.1 2.8 + - - +
420I ARG* 3.0 33.4 + - - +
429I ASP* 5.1 3.3 - - - +
506I PHE 2.8 17.3 + - - -
507I THR* 3.6 8.7 - - - +
601I 1RY 3.5 14.1 - - - -
604I CA 4.1 5.6 - - - -
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Residues in contact with SER 417 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386I ARG* 3.7 7.6 + - - -
415I CYS 3.6 0.2 + - - -
416I GLY* 1.3 69.1 - - - -
418I TYR* 1.3 64.7 + - - +
420I ARG* 3.3 17.5 + - - +
421I GLY 3.2 4.3 + - - -
422I LYS* 3.0 44.1 + - - +
425I CYS* 3.7 13.1 - - - +
427I ASP 4.8 0.2 + - - -
601I 1RY 2.3 43.7 + - - -
604I CA 4.1 3.1 - - - -
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Residues in contact with TYR 418 (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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389I ARG* 2.8 71.9 + - + +
392I ALA* 3.7 17.9 - - + -
393I THR* 2.4 47.0 + - - +
396I GLU* 4.0 13.7 + - - -
414I ALA* 3.4 34.1 - - + -
415I CYS 3.4 9.1 + - - +
416I GLY 3.2 0.2 - - - -
417I SER* 1.3 80.2 + - - +
419I ARG* 1.3 62.6 + - - +
421I GLY* 3.1 6.4 + - - -
425I CYS* 3.7 14.9 - - - -
427I ASP 5.8 2.2 + - - +
428I VAL* 6.1 2.9 - - + -
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Residues in contact with ARG 419 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413I VAL* 5.0 4.6 - - - +
414I ALA 3.3 23.8 - - - +
415I CYS* 3.2 17.2 + - - +
416I GLY 3.1 4.9 + - - +
418I TYR* 1.3 83.4 - - - +
420I ARG* 1.3 59.0 + - - +
421I GLY* 3.2 1.8 + - - -
503I LEU* 3.7 20.6 + - - +
507I THR* 2.6 43.4 + - + +
556I GLU* 3.0 39.8 + - - -
567I TYR* 4.9 2.2 + - - -
570I PRO* 3.2 30.5 - - + +
571I ALA 4.6 0.2 + - - -
573I ARG* 3.6 2.8 - - - +
605I ACT 5.4 3.8 + - - -
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Residues in contact with ARG 420 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416I GLY 3.0 18.6 + - - +
417I SER* 3.3 17.3 + - - +
418I TYR 3.1 0.6 - - - -
419I ARG* 1.3 76.6 - - - +
421I GLY* 1.3 57.9 + - - +
422I LYS* 3.4 18.7 + - - +
507I THR* 2.7 42.7 + - + -
508I GLY 4.0 3.1 - - - -
509I SER* 3.7 22.9 - - - +
570I PRO 3.2 24.7 - - - +
571I ALA* 3.2 23.5 - - - +
573I ARG* 3.8 13.9 - - - -
574I ASP* 2.7 32.4 + - - +
601I 1RY 2.7 31.7 + - - -
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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