Contacts of the helix formed by residues 51 - 62 (chain 2) in PDB entry 5IY6
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 51 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412 CYS* 5.0 6.1 - - + +
422 LEU* 4.0 9.6 - - + -
452 PHE* 3.0 55.8 + - + +
492 PRO* 3.8 5.1 - - + +
502 SER* 1.3 76.2 - - - +
522 ALA* 1.3 58.8 + - - +
532 LYS 3.2 0.7 + - - -
542 ASN* 2.5 30.5 - - - +
552 TRP* 2.9 34.1 - - + +
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Residues in contact with ALA 52 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422 LEU* 3.5 18.4 - - + +
452 PHE 5.2 2.6 + - - +
462 ARG* 6.3 2.7 - - - -
502 SER* 3.3 2.6 - - - -
512 LEU* 1.3 78.6 - - - +
532 LYS* 1.3 56.2 + - - +
552 TRP* 3.1 2.8 + - - -
562 VAL* 2.7 50.6 + - + +
882 GLY* 4.0 13.9 - - - +
912 SER* 3.8 14.1 - - - +
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Residues in contact with LYS 53 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502 SER* 4.2 11.0 + - - +
512 LEU 3.2 2.2 + - - -
522 ALA* 1.3 76.4 - - - +
542 ASN* 1.3 62.8 + - - +
562 VAL* 2.7 26.4 - - + +
572 MET* 3.2 19.7 - - - +
912 SER* 4.8 7.1 + - - -
942 ARG* 3.2 29.5 - - - +
952 ILE* 3.1 36.8 - - + -
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Residues in contact with ASN 54 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502 SER 5.2 0.3 - - - +
512 LEU* 2.5 30.0 - - - +
532 LYS* 1.3 78.2 - - - +
552 TRP* 1.3 93.2 + - - +
572 MET* 3.3 26.4 + - - +
582 ARG* 3.6 11.2 + - - +
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Residues in contact with TRP 55 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382 PRO* 3.9 27.4 - - + +
412 CYS* 3.2 30.1 - - + -
422 LEU* 2.9 29.7 - - + +
512 LEU* 2.9 32.0 - - + +
522 ALA 3.1 1.4 + - - -
542 ASN* 1.3 109.9 - - - +
562 VAL* 1.3 65.1 + - - +
582 ARG* 3.1 25.0 + - + +
592 MET* 3.2 12.8 + - - +
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Residues in contact with VAL 56 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422 LEU* 3.6 18.2 - - + -
522 ALA* 2.7 34.3 + - + +
532 LYS* 2.7 29.8 - - + +
552 TRP* 1.3 71.8 - - - +
572 MET* 1.3 57.9 + - - +
592 MET* 3.1 8.2 + - - +
602 LEU* 2.8 32.4 + - - +
882 GLY 3.9 9.0 - - - +
912 SER* 3.3 26.9 - - - +
922 GLY* 3.9 12.3 - - - +
952 ILE* 3.6 26.0 - - + -
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Residues in contact with MET 57 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532 LYS* 3.2 28.3 - - - +
542 ASN* 3.5 15.7 - - - +
552 TRP 3.1 0.8 - - - -
562 VAL* 1.3 83.6 - - + +
582 ARG* 1.3 65.6 + - + +
602 LEU* 2.9 32.4 + - + +
612 PHE* 3.7 12.5 + - + -
952 ILE* 4.0 23.1 - - + -
992 GLN* 5.4 4.5 - - - +
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Residues in contact with ARG 58 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352 TYR* 4.6 10.3 - - + -
382 PRO* 5.6 7.0 - - + -
542 ASN 3.8 14.1 - - - +
552 TRP* 3.1 21.7 + - + +
572 MET* 1.3 77.8 - - - +
592 MET* 1.3 62.8 + - - +
612 PHE* 3.1 48.6 + - + -
622 LEU 3.9 3.3 + - - -
2193 GLN* 4.3 23.8 - - - +
2213 PRO* 6.3 0.6 - - - +
2223 SER* 3.7 22.9 + - - -
2253 GLN* 5.1 8.7 + - - +
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Residues in contact with MET 59 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352 TYR* 5.2 16.0 - - + +
382 PRO* 3.6 10.3 - - + +
392 ALA* 3.5 36.8 - - + +
422 LEU* 3.1 37.0 - - + -
552 TRP 3.2 5.1 + - - +
562 VAL* 3.2 12.6 - - - +
582 ARG* 1.3 77.4 - - - +
602 LEU* 1.3 68.3 + - + +
612 PHE 3.3 0.3 + - - -
622 LEU 3.6 15.3 + - - +
882 GLY 6.0 1.1 - - - +
922 GLY* 5.8 5.6 - - - -
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Residues in contact with LEU 60 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562 VAL 2.8 29.9 + - - +
572 MET* 2.9 20.6 + - + +
592 MET* 1.3 79.9 - - + +
612 PHE* 1.3 68.1 + - - +
622 LEU 4.5 0.9 - - - -
772 LYS* 5.1 8.6 + - - +
922 GLY* 3.2 33.7 - - - +
952 ILE* 2.9 43.3 - - + -
962 TRP* 3.5 16.7 - - + +
992 GLN* 3.6 27.1 - - + +
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Residues in contact with PHE 61 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352 TYR* 5.3 3.8 - + - -
572 MET* 3.9 11.7 - - + -
582 ARG* 3.1 51.8 - - + -
592 MET 3.3 0.2 - - - -
602 LEU* 1.3 86.3 - - - +
622 LEU* 1.4 69.7 + - + +
992 GLN* 2.9 41.5 - - + -
363 LYS* 3.3 20.9 + - - -
2213 PRO* 4.6 19.5 - - + +
2223 SER* 5.1 9.9 - - - -
2243 LEU* 6.0 9.6 - - + -
2253 GLN* 5.7 7.9 - - + -
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Residues in contact with LEU 62 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312 LEU* 3.6 34.3 - - + +
322 ASP* 5.4 0.7 - - - -
352 TYR* 2.9 78.7 - - + +
582 ARG 3.9 1.4 + - - -
592 MET 3.6 12.7 + - - -
602 LEU 3.5 0.8 - - - -
612 PHE* 1.4 87.7 - - + +
363 LYS* 3.7 39.9 + - + +
2213 PRO* 5.0 4.7 - - + +
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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