Contacts of the helix formed by residues 113 - 120 (chain G) in PDB entry 3SZ9
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 113 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G GLY 4.2 1.1 - - - +
112G LYS* 1.3 90.4 - - + +
114G TYR* 1.3 60.1 + - - +
115G VAL* 4.4 4.9 - - + +
116G ILE* 3.0 30.3 + - + +
117G SER* 2.9 24.6 + - - -
297G ASN* 5.9 1.6 - - - -
298G GLN* 3.3 15.9 - - - +
334G PRO* 3.4 15.0 - - + +
336G ASP 5.8 0.2 - - - +
339G THR* 4.0 15.3 - - + +
340G GLU* 3.6 29.6 - - - +
341G GLN 4.4 0.2 - - - +
342G GLY 4.2 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 114 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G VAL* 3.4 18.6 - - + -
9G PRO* 3.0 29.2 + - - +
11G PRO* 3.4 37.2 - - + +
100G THR* 3.6 20.4 - - - +
103G ALA* 3.7 33.9 - - + -
104G ALA* 3.8 10.3 - - - -
107G THR* 3.1 14.7 + - - +
112G LYS 3.4 0.4 + - - -
113G PRO* 1.3 71.2 - - - +
115G VAL* 1.3 70.3 + - + +
117G SER* 3.2 0.7 + - - -
118G TYR* 2.9 38.4 + + + +
334G PRO 3.0 13.1 + - - +
335G PHE* 3.7 23.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G VAL* 4.6 17.9 - - + -
113G PRO* 3.2 4.4 - - + +
114G TYR* 1.3 86.6 - - + +
116G ILE* 1.3 70.6 + - + +
118G TYR* 3.8 0.9 - - - +
119G LEU* 2.9 48.9 + - + +
334G PRO 4.8 1.0 + - - +
336G ASP 5.4 1.6 - - - +
337G SER* 4.4 30.7 - - - +
339G THR 5.9 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 116 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G LYS* 5.2 5.4 - - + +
113G PRO* 3.0 33.8 + - + +
115G VAL* 1.3 86.4 - - + +
117G SER* 1.3 67.4 + - - +
118G TYR 3.0 0.9 - - - -
119G LEU* 6.1 1.1 - - + -
120G VAL* 2.7 49.8 + - + -
121G ASP* 3.1 14.7 + - - +
296G PHE* 3.9 24.2 - - + -
297G ASN* 6.0 2.0 - - + +
340G GLU* 5.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G ALA* 3.4 27.8 + - - -
106G GLU* 3.9 5.7 - - - +
107G THR* 3.0 22.9 + - - -
112G LYS* 3.1 22.1 - - - +
113G PRO 2.9 6.3 + - - -
114G TYR 3.5 7.9 - - - -
116G ILE* 1.3 77.1 - - - +
118G TYR* 1.3 57.7 + - - +
121G ASP* 3.3 14.4 + - - +
122G LEU* 3.0 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G ALA 4.9 2.7 - - - -
8G VAL* 4.0 17.5 - - + -
9G PRO* 3.3 39.5 - - + +
99G ARG* 2.9 72.3 + - + +
100G THR* 3.8 13.9 + - - -
103G ALA* 3.8 19.1 - - + -
114G TYR* 2.9 32.7 + - + +
115G VAL 3.9 2.5 - - - +
117G SER* 1.3 79.6 - - - +
119G LEU* 1.3 77.5 + - + +
122G LEU* 3.8 6.9 - - - +
123G ASP 3.9 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G ALA 4.7 7.0 - - - +
8G VAL* 3.9 25.4 - - + -
99G ARG* 4.2 5.5 + - - +
115G VAL* 2.9 31.5 + - + +
116G ILE* 5.0 0.9 - - + -
118G TYR* 1.3 92.3 - - + +
120G VAL* 1.3 66.4 + - + +
123G ASP* 3.3 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 120 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G ILE* 2.7 43.9 + - + +
119G LEU* 1.3 79.7 - - + +
121G ASP* 1.3 70.8 + - - +
122G LEU 3.4 0.2 - - - -
123G ASP* 3.4 2.5 + - - +
124G MET* 3.0 49.1 + - - +
170G PHE* 5.9 1.8 - - + -
296G PHE* 4.1 24.9 - - + -
8001G I3E 5.2 3.1 - - + -
----------------------------------------------------------
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