Contacts of the helix formed by residues 118 - 132 (chain U) in PDB entry 6FF7
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 HIS 118 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81U TYR* 4.2 23.1 - - + +
82U SER* 4.7 10.3 - - - -
83U PRO 5.3 2.5 - - - -
115U LYS 4.5 2.8 + - - +
116U PRO 3.4 0.2 - - - -
117U ASP* 1.3 77.3 - - + +
119U PHE* 1.3 59.5 + - - +
120U PRO 3.4 1.8 - - - -
121U PHE* 3.4 12.8 + - + +
122U PHE* 3.1 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 119 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112U PHE* 5.3 12.1 - - + -
115U LYS 5.2 1.7 + - - +
116U PRO* 3.2 20.8 + - + +
118U HIS* 1.3 76.6 - - - +
120U PRO* 1.4 61.6 - - - +
122U PHE* 3.3 6.9 + - - +
123U PHE* 2.8 32.4 + - - +
161U LEU* 5.7 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 120 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116U PRO 4.5 1.8 - - - -
117U ASP 4.6 6.0 - - - +
118U HIS 3.4 0.8 - - - -
119U PHE* 1.4 77.6 - - - +
121U PHE* 1.3 62.7 + - - +
123U PHE* 3.8 5.7 - - + +
124U LYS* 3.1 25.5 + - - +
165U GLN* 5.6 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 121 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83U PRO* 5.1 17.3 - - + -
118U HIS* 3.4 15.3 + - + +
119U PHE 3.3 0.2 - - - -
120U PRO* 1.3 79.2 - - - +
122U PHE* 1.3 64.4 + - - +
124U LYS* 3.5 6.0 + - - +
125U HIS* 3.2 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 122 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91U LEU* 6.1 1.0 - - - +
118U HIS 3.1 18.4 + - - +
119U PHE* 3.3 8.3 + - - +
121U PHE* 1.3 77.1 - - - +
123U PHE* 1.3 61.1 + - - +
125U HIS* 3.2 7.6 + - - +
126U ILE* 3.0 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119U PHE 2.8 21.9 + - - +
120U PRO* 3.8 4.7 - - + +
122U PHE* 1.3 74.4 - - - +
124U LYS* 1.3 62.3 + - - +
126U ILE* 3.1 17.9 + - - +
127U LEU* 3.1 12.0 + - - +
165U GLN* 4.4 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120U PRO 3.1 16.6 + - - +
121U PHE* 3.8 6.5 - - - +
123U PHE* 1.3 76.6 - - - +
125U HIS* 1.3 58.1 + - - +
127U LEU* 3.3 10.2 - - - +
128U LYS* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 125 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86U SER* 6.4 2.7 - - - -
91U LEU* 5.9 2.5 - - - -
121U PHE 3.2 13.3 + - - +
122U PHE* 3.2 6.6 + - - +
123U PHE 3.1 0.6 - - - -
124U LYS* 1.3 75.6 - - - +
126U ILE* 1.3 61.0 + - - +
127U LEU 3.2 0.4 - - - -
128U LYS* 3.8 9.5 - - + +
129U ALA* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91U LEU* 5.9 5.1 - - + +
122U PHE 3.0 12.6 + - - +
123U PHE* 3.3 12.6 - - - +
125U HIS* 1.3 77.6 - - - +
127U LEU* 1.3 57.0 + - - +
129U ALA* 3.3 6.6 + - - +
130U ALA* 2.9 30.2 + - - +
146U LEU* 5.1 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123U PHE 3.1 11.0 + - - +
124U LYS* 3.3 13.7 - - - +
125U HIS 3.2 0.2 - - - -
126U ILE* 1.3 77.1 - - - +
128U LYS* 1.3 61.7 + - - +
130U ALA* 3.2 8.0 + - - +
131U LEU* 3.2 22.7 + - - +
221U PHE* 5.5 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124U LYS 3.1 10.4 + - - +
125U HIS* 3.8 11.4 - - + +
127U LEU* 1.3 78.6 - - - +
129U ALA* 1.3 64.1 + - - +
131U LEU* 3.2 7.1 + - - +
132U ALA* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91U LEU* 5.9 6.1 - - + -
125U HIS 3.1 19.3 + - - +
126U ILE* 3.6 7.2 - - - +
128U LYS* 1.3 76.2 - - - +
130U ALA* 1.3 62.0 + - - +
132U ALA* 3.2 22.2 + - - +
138U PHE* 4.5 8.1 - - - +
143U GLN* 5.1 5.1 - - - +
146U LEU* 5.6 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126U ILE 2.9 16.4 + - - +
127U LEU* 3.2 9.4 + - - +
129U ALA* 1.3 76.8 - - - +
131U LEU* 1.3 58.6 + - - +
132U ALA 3.7 2.4 + - - +
143U GLN* 4.9 13.1 - - - +
146U LEU* 4.5 22.6 - - + +
147U LEU* 5.7 1.1 - - - +
225U LEU* 6.6 0.7 - - + -
228U LYS* 5.5 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127U LEU 3.2 13.9 + - - +
128U LYS* 3.2 6.7 + - - +
129U ALA 3.2 0.2 - - - -
130U ALA* 1.3 74.5 - - - +
132U ALA* 1.3 69.0 + - - +
133U GLU* 3.5 1.9 + - - -
221U PHE 6.2 0.2 - - - +
224U GLN* 5.8 9.0 - - + -
225U LEU* 6.0 6.7 - - + +
228U LYS* 5.5 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128U LYS 3.0 11.6 + - - +
129U ALA* 3.2 21.5 + - - +
130U ALA 3.4 3.1 - - - +
131U LEU* 1.3 80.9 - - - +
133U GLU* 1.3 69.6 + - - +
134U THR* 3.3 3.3 + - - -
137U GLU* 5.5 7.6 - - + +
138U PHE* 4.8 16.4 - - + +
----------------------------------------------------------
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