Contacts of the helix formed by residues 119 - 124 (chain A) in PDB entry 1SAW
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 TRP 119 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLY* 5.2 5.8 - - - -
43A VAL* 4.5 9.2 - - + -
45A PHE* 3.9 29.4 - + + -
109A GLN* 3.2 32.7 - - + +
112A CYS* 3.8 20.2 - - + +
113A LYS* 3.8 24.5 - - + +
117A LEU 3.6 14.3 + - - -
118A PRO* 1.3 71.1 - - + +
120A THR* 1.3 63.1 + - - +
121A LEU 3.5 1.8 - - - -
122A ALA* 3.1 7.4 + - + +
123A LYS* 2.9 35.0 + - + +
124A SER* 4.8 0.7 - - - -
301A CL 3.4 11.6 - - + +
116B GLY 3.3 28.3 + - - -
117B LEU* 4.2 6.9 - - + -
118B PRO* 3.7 42.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PRO* 3.2 6.2 + - - +
119A TRP* 1.3 73.0 - - - +
121A LEU* 1.3 66.7 + - + +
124A SER* 2.8 54.7 + - - -
125A PHE* 4.1 0.5 + - - -
44B LEU* 2.5 44.7 + - + +
45B PHE* 3.3 8.0 - - - +
46B LEU* 4.3 12.8 + - + +
179B ILE* 5.2 1.0 - - + +
180B ILE* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 2.6 54.1 + - + +
105A ALA* 4.2 0.5 - - - +
108A VAL* 3.8 17.9 - - + -
112A CYS* 5.8 1.8 - - - -
118A PRO 4.8 1.4 + - - -
119A TRP 3.5 0.4 - - - -
120A THR* 1.3 87.8 - - - +
122A ALA* 1.3 59.5 + - - +
125A PHE* 3.3 8.7 - - - -
42B PRO 6.1 0.2 - - - +
44B LEU* 4.5 13.7 - - + +
175B TYR* 4.0 17.9 - - - +
179B ILE* 3.7 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A THR* 3.4 8.3 - - - +
105A ALA* 2.9 36.2 + - - +
108A VAL* 3.7 8.5 - - + +
109A GLN* 3.6 41.7 - - + +
112A CYS* 4.7 2.4 - - - -
119A TRP* 3.1 12.6 + - - +
121A LEU* 1.3 80.1 - - - +
123A LYS* 1.3 63.0 + - + +
125A PHE* 3.5 3.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 3.5 38.3 - - + -
47A LYS* 2.7 34.5 + - - +
71A GLU* 3.5 12.9 + - - -
102A ASP* 2.7 37.2 + - - +
103A MET 4.4 2.0 - - - -
104A THR* 2.7 36.9 + - + +
106A ARG* 4.7 0.6 - - - +
109A GLN* 3.7 18.7 - - - +
119A TRP* 2.9 27.9 + - + +
120A THR 3.3 0.2 + - - -
122A ALA* 1.3 83.3 - - + +
124A SER* 1.3 60.6 + - - +
125A PHE* 3.8 4.3 - - - -
128A SER* 3.2 3.2 + - - -
225A MG 3.6 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 4.8 0.3 - - - -
46A LEU 2.6 29.1 + - - -
47A LYS* 4.5 0.9 - - - +
48A PRO* 3.1 30.0 - - - +
119A TRP 4.8 0.3 - - - -
120A THR* 2.8 41.7 + - - -
123A LYS* 1.3 79.0 - - - +
125A PHE* 1.3 61.8 + - - +
128A SER* 3.9 1.6 - - - -
46B LEU* 4.0 5.0 - - - +
179B ILE* 5.4 0.2 - - - -
180B ILE* 3.3 15.1 - - - +
----------------------------------------------------------
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