Contacts of the helix formed by residues 106 - 117 (chain C) in PDB entry 5FHK
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 MET 106 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C THR* 4.2 17.5 - - + -
98C PRO* 3.7 31.9 - - + -
101C LEU* 4.1 9.0 - - + +
102C THR* 2.9 32.2 + - + +
105C MET* 1.3 96.1 - - + +
107C MET* 1.3 65.6 + - - +
108C PRO* 3.3 2.9 - - - -
109C MET* 3.0 25.3 + - + +
110C LEU* 3.0 22.1 + - + +
142C PHE* 4.0 29.8 - - + -
157C ILE* 4.2 10.5 - - - -
264C ILE* 4.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C THR* 3.0 17.1 + - + +
103C LYS* 3.3 22.9 - - - +
106C MET* 1.3 75.3 - - - +
108C PRO* 1.3 58.8 - - + +
110C LEU* 3.9 24.9 - - + -
111C ASN* 2.7 63.4 + - - +
114C MET* 4.8 0.9 - - + -
124C LEU* 4.2 6.3 - - - -
215F PHE* 3.6 27.6 - - + -
222F VAL* 3.5 37.2 - - + +
225F SER* 3.8 15.7 - - - +
226F ALA* 4.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LYS 3.5 14.8 - - - +
104C ARG* 3.6 21.5 - - - +
105C MET 4.2 2.5 - - - +
106C MET 3.4 4.7 - - - +
107C MET* 1.3 87.9 - - + +
109C MET* 1.3 55.7 + - + +
111C ASN* 3.9 8.1 - - + +
112C GLY* 3.0 23.2 + - - -
288C TYR* 3.6 26.1 + - + +
225F SER* 5.6 0.9 - - - +
229F GLU* 6.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C MET* 4.2 18.4 - - + +
106C MET* 3.0 21.3 + - + +
108C PRO* 1.3 75.4 - - + +
110C LEU* 1.3 64.3 + - + +
112C GLY 3.1 1.0 + - - -
113C PHE* 2.8 28.0 + - - +
142C PHE* 4.7 2.5 - - + -
157C ILE* 4.1 28.0 - - + +
281C PHE* 5.8 0.4 - - - -
284C TYR* 3.4 11.1 - - + -
285C VAL* 4.1 34.8 - - + +
288C TYR* 3.6 51.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ILE* 3.9 12.3 - - + -
97C THR* 5.3 1.1 - - + -
106C MET* 3.0 24.3 + - + +
107C MET* 3.8 31.4 - - + +
109C MET* 1.3 76.3 - - + +
111C ASN* 1.3 58.6 + - - +
113C PHE* 3.2 5.6 + - - +
114C MET* 2.8 37.0 + - + +
122C ILE* 4.1 22.0 - - + -
124C LEU* 4.2 25.6 - - + -
142C PHE* 5.3 3.8 - - + -
281C PHE* 3.6 35.2 - - + -
215F PHE* 4.6 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C MET* 2.7 40.4 + - - +
108C PRO* 3.9 6.6 - - + +
110C LEU* 1.3 72.0 - - - +
112C GLY* 1.3 62.2 + - - +
114C MET* 3.3 2.6 + - - +
115C SER* 3.0 25.5 + - - -
225F SER* 3.4 24.9 + - - -
226F ALA* 3.2 22.2 - - - +
229F GLU* 3.4 36.8 - - + +
231F LEU* 3.4 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C PRO 3.0 16.2 + - - -
109C MET 3.1 1.1 + - - -
111C ASN* 1.3 77.5 - - - +
113C PHE* 1.3 61.7 - - - +
115C SER* 3.3 6.0 + - - -
116C GLN* 3.2 21.8 + - - +
284C TYR* 3.1 21.4 + - - -
288C TYR* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ILE* 4.0 7.9 - - + -
109C MET 2.8 16.7 + - - +
110C LEU* 3.5 6.7 - - - +
112C GLY* 1.3 76.2 - - - +
114C MET* 1.3 66.4 + - + +
116C GLN* 3.1 11.2 + - - -
117C TYR* 3.1 40.4 + + - +
120C ILE* 3.7 46.2 - - + -
122C ILE* 4.4 13.0 - - + -
277C LYS 3.9 2.2 - - - -
280C LEU* 3.7 3.4 - - + -
281C PHE* 3.3 51.1 - + + -
284C TYR* 3.3 34.5 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C MET* 4.8 0.4 - - + -
110C LEU* 2.8 25.7 + - + +
111C ASN* 3.9 12.1 - - - +
113C PHE* 1.3 76.3 - - + +
115C SER* 1.3 61.6 + - - +
117C TYR 3.4 18.6 + - - +
120C ILE* 4.8 10.5 - - + +
122C ILE* 3.5 31.9 - - + -
214F ARG* 2.9 41.5 + - - +
215F PHE* 3.9 43.5 - - + -
226F ALA* 4.6 0.9 - - + -
231F LEU* 3.6 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ASN 3.0 16.6 + - - -
112C GLY* 3.7 6.3 - - - -
113C PHE 3.2 0.2 - - - -
114C MET* 1.3 80.5 - - - +
116C GLN* 1.3 60.0 + - - +
117C TYR 3.6 0.2 + - - -
118C PRO* 4.1 10.4 - - - +
214F ARG* 3.9 4.1 + - - +
229F GLU* 5.8 2.9 - - - -
231F LEU* 3.7 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLY 3.2 10.5 + - - +
113C PHE* 3.1 10.0 + - - +
115C SER* 1.3 78.0 - - - +
117C TYR* 1.3 100.9 + - + +
118C PRO* 3.4 8.4 - - - +
284C TYR* 3.5 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ALA* 3.8 20.9 - - + +
113C PHE* 3.1 49.8 + + + +
114C MET* 3.4 9.1 - - - +
116C GLN* 1.3 117.0 + - + +
118C PRO* 1.3 67.1 - - - +
119C GLU 3.0 4.6 + - - -
120C ILE* 3.0 37.5 + - + +
280C LEU* 3.7 37.2 + - + +
284C TYR* 5.0 3.4 - + - -
----------------------------------------------------------
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