Contacts of the strand formed by residues 138 - 142 (chain H) in PDB entry 3AOH
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 SER 138 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H ILE* 3.8 22.7 - - - +
22H GLN* 4.7 7.0 + - - +
136H ILE 3.7 0.4 + - - -
137H VAL* 1.3 80.2 - - - +
139H GLN* 1.3 59.9 + - - +
333H ILE* 3.5 23.3 - - - +
334H ARG 3.6 11.1 + - - -
335H THR* 4.6 4.0 - - - +
336H VAL 5.1 0.8 + - - +
339H LEU* 4.6 0.2 - - - -
391H LEU* 5.1 0.7 - - - +
407H LYS 5.4 1.9 + - - -
408H ARG 5.3 5.0 - - - -
409H ARG 3.3 10.9 + - - +
410H ILE* 3.4 11.7 - - - +
411H SER* 3.2 22.9 + - - -
455H LEU* 6.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 139 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138H SER* 1.3 77.0 - - - +
140H ILE* 1.3 61.8 + - - +
332H ARG 3.2 0.9 - - - +
333H ILE* 2.9 7.4 - - - -
334H ARG* 2.6 60.2 + - + +
339H LEU* 4.5 3.6 - - + +
391H LEU* 3.1 30.6 - - + +
410H ILE* 3.5 6.7 - - - -
411H SER* 3.6 12.9 - - - +
412H ALA 4.6 0.7 - - - +
413H LEU 3.1 23.2 + - - +
414H GLY* 3.2 0.8 - - - -
415H PRO* 2.9 39.9 - - - +
418H LEU* 3.1 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 140 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H GLN* 1.3 76.3 - - - +
141H HIS* 1.3 70.0 + - - +
331H ARG* 3.1 41.7 - - + +
332H ARG 3.1 5.8 - - - +
333H ILE* 2.9 33.0 - - + -
410H ILE* 3.1 24.0 - - + -
411H SER 3.3 12.2 + - - +
412H ALA* 3.6 24.7 - - + +
418H LEU* 3.2 15.3 - - - +
419H THR* 4.1 7.9 - - + -
438H ILE* 5.7 5.2 - - + -
451H LEU 5.5 0.4 - - - +
467H ILE* 5.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 141 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H ILE* 1.3 83.6 - - - +
142H ARG* 1.3 71.2 + - - +
143H SER 2.9 4.7 + - - -
144H PRO* 3.2 29.9 - - + +
165H LEU* 4.1 17.7 - - + +
265H ARG* 4.6 1.1 - - - -
331H ARG* 3.1 23.5 - - - +
332H ARG* 3.4 54.1 + - + +
334H ARG* 4.2 18.8 - - + +
418H LEU* 3.5 30.0 - - + +
419H THR* 5.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141H HIS* 1.3 76.0 - - - +
143H SER* 1.3 65.6 + - - +
144H PRO* 2.9 13.7 - - - +
147H TYR* 2.8 42.4 - - + +
149H THR* 5.2 8.5 - - - +
161H SER* 4.5 18.8 + - - -
163H ILE* 3.8 23.1 - - + +
171H TRP* 6.0 6.8 - - + -
325H ILE* 2.8 59.9 - - + +
330H ASN* 3.6 7.2 - - - -
331H ARG* 4.6 3.6 - - + -
418H LEU* 5.3 8.3 + - - +
----------------------------------------------------------
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