Contacts of the strand formed by residues 38 - 40 (chain P) in PDB entry 1HI0
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 GLU 38 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P ALA 4.2 0.4 + - - -
37P ILE* 1.3 72.3 - - - +
39P THR* 1.3 65.1 + - - +
40P TYR 3.1 12.6 + - - +
41P GLU* 3.6 4.7 - - - +
42P GLY* 2.8 24.3 + - - -
43P LEU 3.4 7.2 - - - +
44P LEU* 4.0 13.2 - - + +
531P GLY* 3.4 5.4 - - - -
532P VAL* 3.0 35.2 + - + +
533P GLN* 5.2 1.4 + - - +
534P SER* 2.8 28.1 + - - -
256Q TYR 4.1 3.4 - - - +
257Q GLY 3.2 26.9 - - - +
258Q ILE* 4.8 2.4 - - - +
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Residues in contact with THR 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P ILE* 3.1 8.4 + - - +
38P GLU* 1.3 71.2 - - - +
40P TYR* 1.3 80.3 + - + +
43P LEU* 3.0 14.5 + - + -
45P SER* 3.4 29.6 - - - -
50P PHE* 3.8 23.6 - - + -
91P ASN* 4.6 1.6 + - - -
525P GLN 4.5 0.7 - - - +
526P PHE 4.4 0.4 - - - +
528P PRO* 3.7 30.5 - - + -
532P VAL* 3.5 0.5 - - - +
544P ARG* 3.0 32.1 + - - +
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Residues in contact with TYR 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P GLU* 3.6 5.0 - - - +
39P THR* 1.3 95.9 - - + +
41P GLU* 1.3 68.5 + - - +
42P GLY 3.1 0.5 + - - -
43P LEU* 2.9 28.1 + - + +
50P PHE* 5.7 0.4 - + - -
524P ASN 4.4 2.3 + - - -
525P GLN* 2.9 41.4 + - - +
526P PHE* 5.0 4.3 - + - -
528P PRO* 5.9 0.2 - - + -
532P VAL* 3.7 9.9 - - - -
544P ARG* 3.6 20.4 + - - -
547P PRO* 4.5 9.0 - - + -
575P TRP* 5.5 2.0 - + - -
583P TYR* 4.6 3.8 - + - -
586P TYR* 3.2 31.6 - + - +
587P ARG* 3.3 35.8 + - - -
590P MET* 3.7 26.2 - - + -
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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
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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