Contacts of the helix formed by residues 521 - 525 (chain D) in PDB entry 4OIN
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 PRO 521 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1090C LYS* 4.3 6.5 - - + -
50D PHE* 4.4 0.4 - - + -
86D ARG 3.3 17.5 - - - +
87D ARG* 3.4 20.4 - - - +
88D TYR 3.2 28.7 - - - +
89D ARG 3.5 13.2 - - - +
90D MET* 3.6 15.5 - - - -
519D VAL 3.6 0.4 - - - +
520D LEU* 1.3 101.1 - - + +
522D PRO* 1.3 71.1 - - + +
523D ASP 3.3 0.2 - - - -
524D LEU* 3.1 19.0 + - + +
525D ARG* 3.6 5.2 - - - +
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Residues in contact with PRO 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU 4.1 2.0 - - - +
45D PHE* 3.7 26.9 - - + -
50D PHE* 3.4 33.7 - - + -
86D ARG* 3.1 40.4 - - - +
520D LEU 3.5 0.4 - - - -
521D PRO* 1.3 84.6 - - + +
523D ASP* 1.3 57.7 + - - +
525D ARG* 2.9 49.9 + - - +
526D PRO* 3.2 4.5 - - - +
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Residues in contact with ASP 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015C LEU 5.1 1.6 - - - +
1016C ILE* 4.1 8.0 - - - +
83D SER 4.5 3.8 - - - +
84D ILE* 5.1 1.4 - - - +
86D ARG* 3.2 49.9 + - - +
87D ARG* 3.6 26.8 + - + +
522D PRO* 1.3 79.4 - - - +
524D LEU* 1.3 60.6 + - - +
525D ARG 3.2 0.2 - - - -
526D PRO* 3.2 22.7 - - - +
337F HIS* 5.9 2.8 - - - -
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Residues in contact with LEU 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1016C ILE* 3.3 31.0 - - + +
1086C ARG 5.5 0.2 - - - -
1087C VAL* 4.0 29.6 - - + +
1090C LYS* 3.7 29.6 - - + -
1091C GLU* 4.7 4.9 - - + +
87D ARG* 3.8 53.2 - - + +
520D LEU* 3.6 26.9 - - + +
521D PRO* 3.1 13.2 + - + +
522D PRO 3.1 1.2 - - - -
523D ASP* 1.3 79.2 - - - +
525D ARG* 1.3 58.6 + - - +
526D PRO* 3.5 2.9 - - - -
538D SER* 5.1 0.9 + - - -
540D LEU* 5.3 1.2 - - - +
606D ILE* 6.0 1.2 - - - +
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Residues in contact with ARG 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 2.9 43.0 + - - +
45D PHE* 3.8 10.9 - - - -
50D PHE* 3.5 6.1 - - - -
519D VAL* 3.4 16.2 - - - +
520D LEU* 2.9 37.2 + - + -
521D PRO 3.6 5.8 - - - +
522D PRO* 3.0 24.1 - - - +
524D LEU* 1.3 79.6 - - - +
526D PRO* 1.3 68.5 - - - +
538D SER* 3.8 22.2 - - - +
540D LEU* 4.2 11.7 - - + -
541D ASN* 3.0 40.6 + - - +
544D TYR* 3.8 24.3 - - - -
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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
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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