Contacts of the strand formed by residues 1104 - 1106 (chain N) in PDB entry 3HOU
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 HIS1104 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224 C 5.1 1.3 - - - -
348M SER 5.9 0.2 - - - -
349M ALA* 3.3 1.6 - - - +
350M ARG* 2.8 38.9 + - + +
370M ILE* 4.2 3.9 - - - +
1102N LYS 2.9 10.5 + - - +
1103N ILE* 1.3 75.8 - - - +
1105N ALA* 1.3 93.7 + - - +
1106N ARG* 4.2 1.2 - - + +
1121N GLY 4.8 0.4 - - - -
1122N ARG* 3.8 43.1 + - + +
1125N ASP* 4.1 16.2 - - - -
1126N GLY 2.8 29.3 + - - -
1127N GLY* 4.8 0.8 - - - -
1128N LEU* 4.2 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1105 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348M SER 3.6 6.7 - - - -
349M ALA* 3.4 15.9 - - + +
370M ILE* 4.0 22.0 - - + -
373M THR* 3.7 27.7 - - - +
374M LEU* 4.6 2.0 - - + -
1104N HIS* 1.3 90.9 + - - +
1106N ARG* 1.3 63.9 + - - +
1125N ASP* 4.2 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1106 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345M VAL 4.9 0.2 - - - +
346M ASP* 2.7 29.7 + - - +
347M PHE* 3.0 6.8 + - - +
348M SER* 2.9 36.0 + - - +
373M THR* 4.3 5.2 - - - -
374M LEU* 3.5 5.4 - - - +
1104N HIS* 4.2 3.4 - - + -
1105N ALA* 1.3 76.6 - - - +
1107N ALA* 1.3 64.7 + - - +
1108N ARG 3.7 7.6 - - - +
1109N GLY* 2.8 28.1 + - - +
1110N PRO* 2.8 33.5 + - - +
1111N MET* 3.1 8.1 - - - +
1118N PRO* 3.5 13.4 - - - +
1119N VAL 4.3 0.8 - - - +
1125N ASP* 2.9 26.8 + - - +
1126N GLY* 3.1 35.2 - - - +
1127N GLY* 3.6 10.3 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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