Contacts of the strand formed by residues 35 - 38 (chain 5) in PDB entry 1O18
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 VAL 35 (chain 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345 ILE* 1.3 80.8 - - - +
365 GLY* 1.3 57.3 + - - +
375 ARG* 3.5 25.4 - - - +
525 SER* 3.5 21.1 - - - +
535 TYR 3.2 6.7 - - - +
545 VAL* 4.2 7.6 - - + -
685 LYS* 3.0 37.5 + - - +
705 PRO* 4.2 1.8 - - + -
815 ASP* 3.4 43.5 - - + +
845 LYS* 4.0 9.2 - - + -
855 ILE* 3.8 13.5 - - + -
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Residues in contact with GLY 36 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355 VAL* 1.3 74.4 - - - +
375 ARG* 1.3 61.5 + - - -
385 PRO* 4.2 0.8 - - - +
525 SER* 3.4 8.7 + - - -
535 TYR* 2.8 35.2 + - - +
585 ALA* 3.9 3.2 - - - +
655 LEU* 3.9 22.9 - - - -
665 THR 3.4 6.7 - - - -
675 LEU* 4.1 8.7 - - - -
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Residues in contact with ARG 37 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355 VAL* 3.5 7.5 - - - +
365 GLY* 1.3 78.2 - - - -
385 PRO* 1.3 68.7 - - + +
515 ASP* 3.6 19.3 + - - +
525 SER* 4.0 5.8 + - - -
655 LEU* 3.7 1.9 - - - +
665 THR* 2.7 42.9 + - - +
685 LYS* 3.1 37.4 - - - +
805 ASP* 3.3 23.4 + - - -
815 ASP* 2.9 21.4 + - - -
845 LYS* 3.4 19.5 - - - +
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Residues in contact with PRO 38 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365 GLY 4.3 1.6 - - - +
375 ARG* 1.3 83.3 - - + +
395 ARG* 1.3 64.5 + - - +
405 HIS* 3.4 17.2 + - - +
415 GLN* 5.6 4.8 - - - +
495 GLN* 5.6 2.9 - - - +
505 LYS 3.7 18.8 - - - +
515 ASP* 3.4 22.4 - - - +
525 SER* 4.5 1.1 - - - +
535 TYR* 5.0 4.0 - - + -
645 ILE* 3.4 13.9 - - + +
655 LEU* 3.6 21.2 - - + -
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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