Contacts of the helix formed by residues 105 - 116 (chain A) in PDB entry 1US1
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 PRO 105 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU 4.0 0.6 - - - +
104A PRO* 1.3 88.6 - - + +
106A LYS* 1.3 63.4 + - - +
107A ALA* 3.6 4.7 + - + +
108A ALA* 3.7 14.3 + - + +
109A ALA* 3.2 18.0 + - - +
120A PRO* 4.5 12.1 - - + -
121A ALA 6.0 0.9 - - - +
639A GLU* 3.2 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PRO 3.8 1.4 + - - -
105A PRO* 1.3 68.4 - - - +
107A ALA* 1.3 72.8 + - - +
109A ALA* 2.9 9.0 + - - +
110A LEU* 3.0 28.1 + - + +
361A TYR* 3.4 40.4 - - + +
529A ASP* 2.9 21.4 + - - -
531A ASP* 3.1 32.6 + - - -
535A LEU* 4.3 2.9 - - + -
637A ARG* 3.5 32.8 - - - +
639A GLU* 3.1 9.7 + - - +
673A ASP* 2.7 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PRO* 5.2 3.1 - - + -
106A LYS* 1.3 82.0 - - - +
108A ALA* 1.3 62.2 - - - +
110A LEU* 3.9 5.6 - - - +
111A ALA* 3.0 20.9 + - - +
115A ARG* 5.0 2.1 + - - -
639A GLU* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PRO* 3.7 16.8 + - + +
106A LYS 3.3 0.6 - - - -
107A ALA* 1.3 79.3 - - - +
109A ALA* 1.3 62.8 + - - +
111A ALA* 3.4 8.8 - - - +
112A HIS* 3.2 21.5 + - - +
118A PRO 4.9 3.5 - - - +
120A PRO* 3.8 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 3.8 26.0 - - + +
60A PHE* 4.5 5.8 - - + -
104A PRO* 4.5 4.9 - - + -
105A PRO 3.2 13.4 + - - +
106A LYS 2.9 8.3 + - - +
108A ALA* 1.3 77.8 - - - +
110A LEU* 1.3 58.2 + - - +
112A HIS* 3.4 4.3 + - - +
113A LEU* 3.1 32.7 + - + +
120A PRO* 4.5 1.6 - - - -
361A TYR* 3.8 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LYS* 3.0 46.1 + - + +
107A ALA* 3.9 3.8 - - - +
109A ALA* 1.3 73.5 - - - +
111A ALA* 1.3 68.1 + - - +
112A HIS 3.0 1.8 - - - -
113A LEU* 4.2 6.5 - - + +
114A ASP* 2.8 35.9 + - - +
115A ARG* 4.9 5.8 - - - +
358A ARG* 3.3 39.5 - - - +
361A TYR* 3.9 20.0 - - + -
531A ASP* 5.0 0.4 - - - +
535A LEU* 4.1 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ALA 3.0 14.5 + - - +
108A ALA* 3.4 15.3 - - - +
110A LEU* 1.3 76.0 - - - +
112A HIS* 1.3 55.3 + - - +
115A ARG* 3.2 48.6 + - - +
116A GLY 3.2 0.2 + - - -
117A SER* 3.2 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY* 3.4 26.9 - - - -
56A GLN 4.7 0.7 - - - -
57A SER* 3.1 31.5 + - - -
59A LEU* 4.0 18.2 - - + -
108A ALA 3.2 9.0 + - - +
109A ALA* 3.4 9.0 - - - +
110A LEU 3.0 0.6 - - - -
111A ALA* 1.3 78.1 - - - +
113A LEU* 1.3 76.1 + - + +
116A GLY* 3.2 16.2 + - - -
117A SER* 2.9 29.0 + - - +
118A PRO 4.3 0.9 - - - +
119A PRO* 3.2 42.0 - - + -
120A PRO* 4.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY 3.9 31.1 + - - +
57A SER 4.5 11.9 - - - +
59A LEU* 4.8 6.3 - - + -
60A PHE* 4.0 28.5 - - + -
109A ALA* 3.1 23.8 + - + +
110A LEU* 4.0 8.7 - - + +
112A HIS* 1.3 89.5 - - + +
114A ASP* 1.3 62.0 + - - +
329A ARG* 5.5 3.4 - - - +
351A ASP* 3.8 18.2 - - - +
353A ARG* 3.6 31.6 + - - +
358A ARG* 4.3 9.0 - - - +
361A TYR* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY 5.9 0.7 - - - -
110A LEU* 2.8 24.4 + - - +
113A LEU* 1.3 80.7 - - - +
115A ARG* 1.3 73.4 + - + +
116A GLY 3.5 1.2 + - - -
353A ARG* 4.8 2.1 + - - -
358A ARG* 2.9 42.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ALA 5.0 2.0 + - - -
110A LEU* 3.8 4.4 + - - +
111A ALA* 3.2 45.1 + - - +
114A ASP* 1.3 90.8 + - + +
116A GLY* 1.3 55.9 + - - +
117A SER* 3.2 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY* 4.8 11.5 - - - +
111A ALA 3.2 2.4 + - - -
112A HIS* 3.2 15.1 + - - -
113A LEU 4.8 0.2 - - - -
114A ASP 3.5 2.2 - - - -
115A ARG* 1.3 74.4 - - - +
117A SER* 1.3 68.4 + - - +
----------------------------------------------------------
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