Contacts of the helix formed by residues 110 - 120 (chain O) in PDB entry 5C7O
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 ASP 110 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108O PHE 5.7 0.2 - - - +
109O ILE* 1.3 74.9 - - - +
111O PRO* 1.3 73.4 - - + +
112O GLU* 3.3 12.1 + - - +
113O TYR* 3.1 36.5 + - - +
114O MET* 2.8 27.5 + - - +
149O GLN* 3.4 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 111 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110O ASP* 1.3 89.3 - - + +
112O GLU* 1.3 62.9 + - - +
114O MET* 3.2 10.7 + - + +
115O VAL* 3.1 25.5 + - - +
133O PHE* 4.0 20.3 - - + +
136O GLY* 3.9 24.5 - - - +
137O GLN 4.3 9.6 - - - +
138O LEU* 4.6 2.0 - - + +
147O VAL* 3.9 28.0 - - + +
149O GLN* 4.6 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110O ASP* 3.3 9.9 + - - +
111O PRO* 1.3 79.0 - - - +
113O TYR* 1.3 61.6 + - - +
115O VAL* 3.3 16.7 + - + +
116O TYR* 3.5 6.9 + - - +
133O PHE* 3.5 48.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 113 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108O PHE 4.0 16.8 - - - -
109O ILE* 3.7 16.8 - - + -
110O ASP* 3.1 28.5 + - - +
112O GLU* 1.3 74.2 - - - +
114O MET* 1.3 65.4 + - - +
116O TYR* 3.1 26.5 + + + -
117O MET* 3.0 54.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 114 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83O PHE* 3.9 22.9 - - + -
104O VAL* 3.6 32.3 - - + +
106O ASP* 4.0 18.2 - - + +
109O ILE* 3.4 32.7 - - + +
110O ASP 2.8 18.7 + - - +
111O PRO* 3.2 8.9 + - + +
113O TYR* 1.3 70.9 - - - +
115O VAL* 1.3 65.7 + - - +
117O MET* 3.8 1.5 - - - +
118O PHE* 2.9 28.2 + - - +
138O LEU* 4.4 17.3 - - + -
147O VAL* 3.6 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111O PRO 3.1 15.4 + - - +
112O GLU* 3.4 9.0 - - - +
113O TYR 3.2 0.2 - - - -
114O MET* 1.3 77.5 - - - +
116O TYR* 1.3 59.4 + - - +
119O LYS* 2.9 48.0 + - - +
131O VAL* 3.5 33.1 - - + +
132O GLU* 3.4 33.4 - - - +
133O PHE* 3.7 12.8 - - + +
138O LEU* 3.7 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 116 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112O GLU 3.5 7.4 + - - +
113O TYR* 3.1 36.4 + + + +
115O VAL* 1.3 82.5 - - - +
117O MET* 1.3 68.6 + - + +
119O LYS* 4.6 4.7 - - - +
120O TYR* 3.2 60.4 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 117 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83O PHE* 5.0 0.7 - - + -
88O ARG* 3.3 52.2 + - - +
109O ILE* 3.5 35.7 - - + -
113O TYR* 3.0 54.3 + - + +
114O MET* 4.0 4.7 - - - +
116O TYR* 1.3 82.4 - - + +
118O PHE* 1.3 58.5 + - - +
120O TYR 3.0 18.7 - - - +
121O ASP* 4.9 2.4 - - - +
501O NAD 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 118 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83O PHE* 3.9 16.4 - + + -
88O ARG* 3.5 31.4 - - + +
91O LEU* 3.5 32.8 - - + -
92O ARG* 3.2 34.4 + - + -
95O MET* 4.8 0.7 - - + -
114O MET 2.9 18.3 + - - +
115O VAL 3.9 2.0 - - - +
117O MET* 1.3 77.8 - - - +
119O LYS* 1.3 62.9 + - - +
120O TYR 4.5 0.2 - - - +
127O TYR* 3.6 40.0 - + - +
131O VAL* 3.8 22.0 - - + -
138O LEU* 5.3 2.0 - - + -
140O VAL* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92O ARG* 3.9 0.3 + - - -
115O VAL* 2.9 30.3 + - - +
116O TYR* 3.4 4.9 + - - +
118O PHE* 1.3 79.5 - - - +
120O TYR* 1.3 88.9 + - + +
126O ARG* 3.2 11.2 - - + +
127O TYR* 2.8 39.7 + - + +
131O VAL* 3.3 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 120 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88O ARG* 5.8 0.2 + - - -
116O TYR* 3.2 47.3 + + + +
117O MET* 3.0 21.4 - - - +
118O PHE 4.6 0.2 - - - -
119O LYS* 1.3 105.0 - - + +
121O ASP* 1.3 61.3 + - - +
126O ARG* 3.7 49.9 + - + +
----------------------------------------------------------
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