Contacts of the helix formed by residues 110 - 118 (chain C) in PDB entry 6UZA
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 ASN 110 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ALA* 2.9 25.7 + - + +
108C TYR* 3.6 1.7 + - + -
109C GLY* 1.3 71.9 - - - +
111C ILE* 1.3 64.2 + - - +
112C PRO* 3.6 13.2 - - - +
113C VAL* 3.4 30.3 + - - +
114C VAL* 3.2 26.3 + - - +
148C ILE* 4.5 0.4 - - - -
896C TYR* 3.8 42.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLY* 2.9 11.7 + - - +
110C ASN* 1.3 71.6 - - - +
112C PRO* 1.4 65.2 - - + +
114C VAL* 3.3 4.3 + - - +
115C ARG* 2.9 46.4 + - - +
147C GLU* 3.3 41.5 - - + +
148C ILE* 3.8 21.5 - - + -
151C LEU* 4.3 13.9 - - + +
893C SER* 3.6 17.0 - - - +
896C TYR* 5.0 0.4 - - - +
897C GLU* 3.6 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ASN* 3.6 12.8 - - - +
111C ILE* 1.4 92.3 - - + +
113C VAL* 1.3 57.2 + - + +
115C ARG* 3.3 21.3 + - + +
116C LYS* 2.9 28.9 + - - +
896C TYR 4.6 11.4 - - - +
897C GLU* 4.8 5.8 - - - -
900C GLU* 3.4 51.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ARG* 3.9 21.1 - - + +
105C ALA* 3.8 16.2 - - + -
110C ASN* 3.4 34.9 + - - +
111C ILE 3.3 0.4 - - - -
112C PRO* 1.3 78.2 - - + +
114C VAL* 1.3 57.3 + - - +
116C LYS* 3.3 9.3 + - - +
117C MET* 2.9 52.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PHE* 4.1 27.0 - - + -
105C ALA* 3.8 28.5 - - + +
106C ALA* 4.1 8.1 - - + +
110C ASN 3.2 16.7 + - - +
111C ILE* 3.7 8.5 - - - +
112C PRO 3.3 0.2 - - - -
113C VAL* 1.3 77.1 - - - +
115C ARG* 1.3 56.3 + - - +
117C MET* 4.9 0.2 - - - -
118C LEU* 2.9 44.7 + - + +
148C ILE* 4.3 18.2 - - + -
151C LEU* 3.7 18.8 - - + -
152C LEU* 5.0 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ILE* 2.9 28.3 + - - +
112C PRO* 3.6 32.6 - - + +
114C VAL* 1.3 78.9 - - - +
116C LYS* 1.3 59.9 + - - +
118C LEU* 4.3 2.6 - - - +
119C GLU* 3.7 21.1 + - - +
151C LEU* 3.7 31.9 - - + -
897C GLU* 4.7 12.7 + - - +
900C GLU* 4.4 8.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ARG* 3.1 31.2 - - - +
112C PRO 2.9 17.3 + - - +
113C VAL* 3.8 12.4 - - - +
114C VAL 3.2 0.2 - - - -
115C ARG* 1.3 77.4 - - - +
117C MET* 1.3 78.2 + - - +
119C GLU* 3.5 0.8 + - - +
120C GLU* 2.9 45.4 + - + +
121C CYS* 5.1 3.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C GLU* 3.3 30.1 - - + +
101C ARG* 3.4 28.5 - - - +
102C PHE* 3.7 41.7 - - + +
113C VAL* 2.9 35.6 + - - +
116C LYS* 1.3 91.4 - - - +
118C LEU* 1.3 59.2 + - - +
119C GLU 3.3 0.2 - - - -
121C CYS* 3.3 40.6 + - - +
124C LEU* 3.5 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PHE* 3.8 20.6 - - + -
114C VAL* 2.9 23.9 + - + +
115C ARG* 4.4 3.8 - - - +
117C MET* 1.3 77.8 - - - +
119C GLU* 1.3 58.4 + - - +
121C CYS 5.1 2.9 - - - -
124C LEU* 4.9 1.1 - - + -
126C VAL* 3.8 28.7 - - + -
151C LEU* 3.5 41.7 - - + +
152C LEU* 4.1 10.5 - - + -
155C LYS* 3.2 40.9 + - - +
----------------------------------------------------------
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