Contacts of the helix formed by residues 103 - 115 (chain B) in PDB entry 1MHQ
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 LYS 103 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TRP* 5.8 3.8 - - + -
99B SER* 3.2 23.1 - - - +
100B GLU* 2.5 43.5 + - - +
102B ALA* 1.3 80.1 - - - +
104B PHE* 1.3 66.8 + - - +
105B ARG* 3.1 11.4 - - + +
106B PHE* 3.0 6.2 + - - +
107B LEU* 2.9 24.0 + - - +
147B LYS* 4.3 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ALA 4.0 0.4 + - - -
103B LYS* 1.3 72.9 - - - +
105B ARG* 1.3 56.9 + - - +
107B LEU* 3.8 9.1 - - + +
108B ASN* 2.8 54.0 + - - +
147B LYS* 3.7 52.5 - - + +
150B ASP* 5.0 14.6 - - + -
151B ALA* 5.7 3.4 - - + -
154B MET* 6.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 4.6 41.3 + - + +
121A SER 6.2 0.6 - - - -
122A TRP* 3.5 34.8 - - - +
65B TRP* 3.2 58.0 - - + +
103B LYS* 3.1 9.0 - - + +
104B PHE* 1.3 81.7 - - - +
106B PHE* 1.3 61.3 + - - +
108B ASN* 3.7 9.8 + - - +
109B GLU* 3.7 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PRO* 3.3 44.6 - - + -
65B TRP* 3.5 16.4 - + + -
67B LEU* 5.1 2.5 - - + -
68B ALA* 4.1 12.8 - - + -
71B ILE* 4.6 9.4 - - + -
86B LEU* 4.3 12.3 - - + -
100B GLU 3.8 11.7 - - - +
101B VAL* 3.3 44.6 - - + +
103B LYS* 3.0 5.2 + - - +
105B ARG* 1.3 75.9 - - - +
107B LEU* 1.3 67.7 + - - +
108B ASN 3.0 1.6 - - - -
109B GLU* 2.9 15.7 + - + +
110B LEU* 3.4 45.1 + - + +
138B TRP* 4.0 6.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL 3.8 14.6 - - - +
102B ALA 3.7 15.5 - - - +
103B LYS 2.9 17.5 + - - +
104B PHE* 3.8 9.0 - - + +
106B PHE* 1.3 76.9 - - - +
108B ASN* 1.3 58.5 + - - +
110B LEU* 3.2 8.3 + - + +
111B ILE* 3.0 31.7 + - + +
135B LEU* 4.0 27.3 - - + +
138B TRP* 4.5 8.7 - - + -
147B LYS* 3.5 38.6 - - + +
148B ILE* 3.8 15.7 - - + +
151B ALA* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PHE* 2.8 45.3 + - - +
105B ARG* 3.8 8.8 - - - +
106B PHE 3.0 0.2 - - - -
107B LEU* 1.3 76.7 - - - +
109B GLU* 1.3 70.8 + - - +
111B ILE* 3.4 19.6 + - - +
112B LYS* 3.0 26.2 + - - +
154B MET* 5.9 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TRP* 4.0 16.7 - - + -
65B TRP* 4.4 9.2 - - + -
68B ALA* 3.8 26.0 - - + -
72B GLN* 2.4 42.4 + - - +
105B ARG* 3.7 18.0 + - - +
106B PHE* 2.9 9.0 + - + +
108B ASN* 1.3 81.0 - - - +
110B LEU* 1.3 64.2 + - + +
112B LYS* 2.7 44.6 + - - +
113B VAL* 3.3 9.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA* 6.4 0.7 - - - -
71B ILE* 4.5 24.9 - - + -
83B LEU* 5.2 1.8 - - + -
86B LEU* 4.9 5.8 - - + -
106B PHE* 3.5 42.6 - - + +
107B LEU* 3.2 11.8 + - + +
108B ASN 3.2 0.4 - - - -
109B GLU* 1.3 77.3 - - + +
111B ILE* 1.3 65.8 + - + +
113B VAL* 3.0 20.8 + - - +
114B LEU* 3.4 14.1 - - + +
131B VAL* 4.2 22.1 - - + +
134B ILE* 5.7 3.6 - - + -
135B LEU* 4.1 22.2 - - + -
138B TRP* 4.0 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 3.0 21.9 + - + +
108B ASN* 3.7 20.9 - - - +
110B LEU* 1.3 76.7 - - + +
112B LYS* 1.3 62.2 + - - +
114B LEU* 3.1 20.3 + - - +
115B SER* 3.0 26.5 + - - +
135B LEU* 5.6 1.6 - - + -
151B ALA* 4.1 23.8 - - + -
154B MET* 4.3 24.7 - - + -
155B LEU* 3.6 35.4 - - + +
158B GLN* 6.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LYS* 6.2 2.9 - - - +
72B GLN* 3.9 13.2 + - - +
108B ASN* 3.0 13.2 + - - +
109B GLU* 2.7 50.7 + - - +
110B LEU 3.1 0.2 - - - -
111B ILE* 1.3 79.3 - - - +
113B VAL* 1.3 59.6 + - - +
115B SER* 3.3 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 4.0 20.9 - - + +
72B GLN* 3.6 26.7 - - + -
109B GLU 3.4 15.7 - - - +
110B LEU* 3.0 11.4 + - - +
112B LYS* 1.3 77.6 - - - +
114B LEU* 1.3 61.7 + - + +
115B SER 3.6 2.3 + - - +
121B SER* 4.8 1.7 - - - -
123B ALA* 3.5 34.4 - - + +
127B VAL* 4.1 16.6 - - + -
128B LYS* 3.5 10.8 - - + +
131B VAL* 4.2 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 3.4 17.7 - - + +
111B ILE* 3.1 10.0 + - - +
113B VAL* 1.3 76.8 - - - +
115B SER* 1.3 63.0 + - - +
116B PRO* 3.5 7.4 - - - +
128B LYS* 3.7 45.0 + - + +
131B VAL* 3.7 29.2 - - + -
132B ILE* 3.9 16.4 - - + +
135B LEU* 5.1 2.0 - - + -
155B LEU* 3.6 32.3 - - + -
160B ILE* 3.6 26.2 - - + +
161B ILE* 5.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ILE* 3.0 23.8 + - - +
112B LYS* 3.7 20.5 - - - +
113B VAL 3.3 1.9 - - - +
114B LEU* 1.3 77.2 - - - +
116B PRO* 1.3 72.2 - - - +
121B SER* 3.6 15.7 - - - -
128B LYS* 4.9 0.2 - - - -
160B ILE* 5.1 5.9 - - - +
----------------------------------------------------------
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