Contacts of the helix formed by residues 113 - 123 (chain F) in PDB entry 4DVQ
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 LEU 113 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F MET 3.2 8.4 + - - +
112F ILE* 1.3 68.9 - - - +
114F GLU* 1.3 67.3 + - - +
115F PRO* 4.0 9.2 - - + -
116F TRP* 3.2 50.1 + - + +
117F VAL* 3.2 23.9 + - - +
130F PHE* 4.7 7.9 - - + -
131F LEU* 4.2 14.0 - - + +
234F THR* 4.3 3.4 - - + -
238F MET* 4.3 28.3 - - + -
487F PHE* 3.9 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 114 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F ILE* 2.9 20.5 + - + +
113F LEU* 1.3 71.6 - - - +
115F PRO* 1.3 66.4 - - + +
116F TRP 3.3 0.2 + - - -
117F VAL* 3.3 6.0 + - + +
118F ALA* 2.8 32.6 + - + +
121F GLN* 6.2 1.8 - - - +
237F LEU 6.1 0.2 - - - +
240F MET 6.1 0.7 - - - +
241F PRO* 5.0 3.2 - - - +
242F ARG* 3.3 45.7 + - + +
253F TRP* 5.2 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 115 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F LEU* 3.4 16.4 - - + -
114F GLU* 1.3 95.0 - - + +
116F TRP* 1.3 63.4 + - + +
118F ALA* 3.4 3.5 - - - +
119F TYR* 3.3 16.8 + - - +
234F THR* 4.6 5.2 - - + +
237F LEU* 3.9 33.4 - - + +
238F MET* 4.4 9.2 - - + +
253F TRP* 3.8 21.5 - - + -
256F HIS* 3.6 36.1 + - + +
257F PHE* 4.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 116 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F LEU* 3.2 25.2 + - + +
114F GLU 3.3 0.4 - - - -
115F PRO* 1.3 75.9 - - + +
117F VAL* 1.3 65.5 + - - +
119F TYR* 3.3 7.8 + - - +
120F ARG* 3.1 35.9 + - - +
130F PHE* 3.7 28.0 - + - -
131F LEU* 3.7 20.4 - - + -
230F MET* 3.5 22.2 - - + -
231F PHE* 4.2 0.4 - + - -
234F THR* 2.9 21.0 + - + +
256F HIS* 3.7 16.8 - + - -
260F TRP* 3.5 25.6 - + - +
487F PHE* 3.5 32.3 - + - -
602F 1CA 3.7 41.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F ILE* 3.9 33.4 - - + -
113F LEU 3.2 16.6 + - - +
114F GLU* 3.9 5.2 - - + +
116F TRP* 1.3 73.1 - - - +
118F ALA* 1.3 66.4 + - - +
120F ARG* 2.9 20.6 + - + +
121F GLN* 3.0 35.1 + - + +
127F CYS* 4.6 11.7 - - - -
131F LEU* 4.3 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F GLU* 2.8 20.0 + - + +
115F PRO 3.4 7.4 - - - +
117F VAL* 1.3 77.8 - - - +
119F TYR* 1.3 56.6 + - - +
121F GLN* 3.4 18.9 - - - +
122F HIS* 3.0 28.9 + - - +
242F ARG* 4.0 17.6 + - - +
253F TRP* 3.8 21.3 - - + -
257F PHE* 3.9 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F PRO 3.3 4.9 + - - +
116F TRP 3.3 10.1 + - - +
117F VAL 3.1 0.8 - - - -
118F ALA* 1.3 76.5 - - - +
120F ARG* 1.3 72.0 + - - +
122F HIS* 3.2 1.7 + - - +
123F ARG* 3.1 42.9 + - + +
125F HIS* 4.4 2.0 + + - -
257F PHE* 3.4 43.0 - + + -
260F TRP* 3.4 42.9 + + + -
261F ASP* 2.3 43.0 + - - -
264F PHE* 3.7 38.8 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F TRP* 3.1 33.3 + - - +
117F VAL* 2.9 8.2 + - - +
119F TYR* 1.3 81.8 - - - +
121F GLN* 1.3 57.9 + - + +
123F ARG 3.4 0.5 + - - -
124F GLY 2.9 8.3 + - - -
125F HIS* 2.7 48.6 + - - +
126F LYS 4.5 10.0 + - - +
127F CYS* 3.7 30.2 - - - +
128F GLY 5.5 1.4 - - - +
131F LEU* 3.5 21.5 - - + +
260F TRP* 3.7 47.1 - - - +
264F PHE* 3.8 29.0 - - - -
309F MET* 5.9 2.6 - - - +
310F GLU* 4.6 15.8 + - - +
602F 1CA 4.8 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F GLU* 6.2 1.8 - - - +
117F VAL* 3.0 31.6 + - + +
118F ALA* 3.4 28.1 - - - +
120F ARG* 1.3 75.2 - - - +
122F HIS* 1.3 63.4 + - - +
124F GLY* 3.7 9.6 + - - +
125F HIS 4.9 1.8 - - - -
242F ARG* 5.7 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 122 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F ALA 3.0 19.4 + - - +
119F TYR* 3.6 4.5 - - + +
120F ARG 3.2 0.4 - - - -
121F GLN* 1.3 80.9 - - - +
123F ARG* 1.3 89.6 + - + +
124F GLY 3.4 0.8 + - - -
242F ARG* 5.6 5.2 - - - +
257F PHE* 3.7 32.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F TYR* 3.1 36.6 + - + +
122F HIS* 1.3 100.9 + - - +
124F GLY* 1.3 64.0 + - - +
125F HIS* 3.4 34.2 + - + +
257F PHE* 5.8 4.8 - - - +
261F ASP* 2.9 34.9 + - - -
----------------------------------------------------------
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