Contacts of the helix formed by residues 104 - 112 (chain H) in PDB entry 1M8V
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 ARG 104 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H GLU* 1.3 82.9 - - + +
105H PRO* 1.3 79.0 - - + +
106H LEU 3.3 1.6 - - - +
107H ASP* 2.7 56.2 + - - +
108H VAL* 2.9 9.9 + - - +
234I TYR 4.2 6.1 - - - +
235I ASP* 5.9 0.9 - - + -
241I VAL* 3.9 0.2 - - - -
2Q U 3.0 25.2 + - - +
3Q U 3.2 33.3 + - - -
1R U 3.7 41.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 105 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H ARG* 1.3 86.6 - - + +
106H LEU* 1.3 60.7 + - + +
108H VAL* 3.2 2.8 + - - +
109H ILE* 2.8 37.2 + - + +
138H LEU* 5.8 1.8 - - + -
234I TYR 3.7 18.8 - - - +
235I ASP* 3.5 24.9 - - + +
239I ASN* 3.7 29.8 - - + +
240I VAL 4.5 0.2 - - - +
241I VAL* 3.6 23.5 - - + -
261I VAL* 4.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H ARG* 3.3 2.0 - - + +
105H PRO* 1.3 79.5 - - + +
107H ASP* 1.3 58.4 + - - +
109H ILE* 4.1 6.1 - - + -
110H HIS* 2.7 37.7 + - - +
134H TYR* 3.8 29.8 - - + -
135H ASP 4.4 4.3 - - - +
136H ILE* 3.5 30.7 - - + -
138H LEU* 4.2 23.3 - - + -
235I ASP* 5.7 2.7 - - - +
1Q U 5.3 1.1 - - - +
2Q U 3.8 37.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 107 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H GLU* 3.6 16.4 + - - +
104H ARG* 2.7 57.4 + - - +
106H LEU* 1.3 73.9 - - - +
108H VAL* 1.3 59.4 + - - +
110H HIS* 3.8 1.0 - - - +
111H ARG* 2.9 42.1 + - - +
2Q U 2.7 42.5 + - - +
3Q U 5.2 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 108 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H GLU* 3.7 20.0 - - - +
104H ARG 2.9 11.2 + - - +
105H PRO 3.5 7.0 - - - +
107H ASP* 1.3 78.0 - - - +
109H ILE* 1.3 62.0 + - + +
111H ARG* 3.3 19.8 + - - +
112H SER* 3.0 28.5 + - - +
172H PRO* 3.7 26.7 - - + -
241I VAL* 3.9 23.8 - - + -
259I LYS* 4.0 13.0 - - + -
261I VAL* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H PRO* 2.8 23.5 + - + +
106H LEU* 4.0 7.6 - - + +
108H VAL* 1.3 77.2 - - + +
110H HIS* 1.3 61.0 + - - +
112H SER* 3.7 7.6 + - - -
113H LEU* 3.9 1.6 + - - +
131H LEU* 3.4 28.9 - - + +
134H TYR* 4.1 31.9 - - + -
138H LEU* 3.7 33.0 - - + -
140H VAL* 5.3 6.5 - - + -
170H ILE* 4.5 20.2 - - + -
261I VAL* 4.0 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 110 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H LEU 2.7 23.3 + - - +
107H ASP 3.8 2.2 - - - +
109H ILE* 1.3 71.4 - - - +
111H ARG* 1.3 67.9 + - + +
112H SER 3.2 0.8 + - - -
113H LEU* 3.4 35.0 + - + +
134H TYR* 2.8 33.6 + - - +
1Q U 3.5 28.8 + + - -
2Q U 3.1 50.8 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 111 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H GLU 3.8 25.7 - - - +
107H ASP* 2.9 30.6 + - - +
108H VAL* 3.3 17.3 + - - +
110H HIS* 1.3 82.7 - - + +
112H SER* 1.3 57.3 + - - +
113H LEU* 3.3 2.1 + - - +
115H LYS* 3.2 26.3 + - - +
259I LYS* 3.3 29.3 - - - +
2Q U 5.4 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H VAL* 3.0 17.3 + - - +
109H ILE* 3.7 9.4 + - - -
110H HIS 3.2 0.6 - - - -
111H ARG* 1.3 76.1 - - - +
113H LEU* 1.3 68.7 + - - +
114H ASP 3.3 0.2 + - - -
115H LYS* 2.8 35.4 + - - +
117H VAL* 3.9 22.2 - - - -
131H LEU* 3.9 7.7 - - - +
172H PRO* 3.5 25.2 - - - +
----------------------------------------------------------
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