Contacts of the helix formed by residues 135 - 146 (chain C) in PDB entry 5SWW
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 LEU 135 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PHE* 3.2 44.5 - - + +
103C SER* 3.7 15.5 - - - +
133C ASP* 3.0 7.9 + - - -
134C PRO* 1.3 88.6 - - + +
136C TYR* 1.3 57.9 + - - +
137C LYS 3.2 2.0 - - - -
138C GLU* 3.2 33.3 + - + +
139C ALA 2.9 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C SER* 5.0 4.7 - - - +
100C PRO 5.4 1.8 - - - +
101C CYS* 6.0 0.7 - - - +
129C ILE* 3.5 20.9 - - + -
130C TYR* 3.3 22.7 - - + +
131C ASP* 3.6 19.5 - - + -
133C ASP* 3.1 25.5 + - + +
134C PRO* 4.3 8.3 - - + -
135C LEU* 1.3 73.3 - - - +
137C LYS* 1.3 109.8 + - + +
139C ALA* 3.1 9.8 + - - +
140C LEU* 2.9 27.8 + - + +
189C ARG* 3.1 31.2 + - - -
193C ILE* 3.9 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C PRO 4.6 10.5 + - - -
136C TYR* 1.3 114.2 - - + +
138C GLU* 1.3 74.1 + - - +
140C LEU 3.3 1.3 + - - +
141C GLN* 2.9 43.8 + - - +
193C ILE* 3.6 34.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PHE* 3.8 22.9 - - + -
135C LEU* 3.2 46.3 + - + +
137C LYS* 1.3 96.4 + - - +
139C ALA* 1.3 56.9 + - - +
141C GLN* 3.9 14.7 - - - +
142C MET* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C PRO 3.3 26.7 - - - +
101C CYS 3.7 7.4 - - - +
102C PHE* 3.5 28.2 - - + +
107C ALA* 3.9 4.4 - - + +
135C LEU 2.9 6.9 + - - +
136C TYR* 3.1 12.1 + - - +
138C GLU* 1.3 75.1 - - - +
140C LEU* 1.3 61.1 + - + +
142C MET* 3.3 3.1 + - - +
143C LEU* 2.9 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C SER* 3.9 26.2 - - - +
100C PRO* 5.1 2.9 - - + +
129C ILE* 4.6 13.5 - - + -
136C TYR* 2.9 27.5 + - + +
137C LYS 3.8 2.9 - - - +
139C ALA* 1.3 76.2 - - + +
141C GLN* 1.3 57.4 + - - +
143C LEU* 3.3 13.0 + - + +
144C ARG* 2.9 28.8 + - - +
150C VAL* 3.7 26.1 - - + +
152C ILE* 6.4 1.3 - - + -
190C LEU* 3.7 29.4 - - + -
193C ILE* 3.8 27.4 - - + -
194C LEU* 3.9 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C LYS* 2.9 28.5 + - - +
138C GLU* 3.9 17.9 - - - +
140C LEU* 1.3 76.9 - - - +
142C MET* 1.3 57.1 + - - +
144C ARG* 3.3 20.6 + - - +
145C ASP* 2.9 39.0 + - - +
193C ILE* 3.3 36.8 + - + +
194C LEU* 4.0 7.6 - - + -
196C ASN* 5.8 3.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PHE* 3.5 24.7 - - + -
107C ALA* 3.7 37.2 - - + +
108C GLY* 3.7 10.8 - - - -
111C ARG* 3.6 45.1 - - + +
138C GLU 2.9 18.0 + - - +
139C ALA 3.7 3.1 - - - +
141C GLN* 1.3 76.9 - - - +
143C LEU* 1.3 63.4 + - - +
145C ASP* 3.4 8.2 + - - +
146C ALA* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C PRO* 3.7 37.9 - - + +
107C ALA* 4.1 16.8 - - + +
110C VAL* 3.7 37.7 - - + -
111C ARG* 5.2 0.9 - - + +
124C ILE* 3.7 17.7 - - + -
139C ALA 2.9 25.9 + - - +
140C LEU* 3.6 12.3 - - + +
142C MET* 1.3 76.3 - - - +
144C ARG* 1.3 62.1 + - - +
146C ALA* 3.4 9.9 + - + +
148C ALA* 3.2 29.1 + - + +
150C VAL* 3.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C LEU 2.9 16.7 + - - +
141C GLN* 3.6 20.2 + - - +
142C MET 3.3 0.2 - - - -
143C LEU* 1.3 78.3 - - - +
145C ASP* 1.3 87.5 + - - +
146C ALA 3.1 1.6 + - - -
147C GLY* 3.1 14.6 + - - -
148C ALA 3.5 11.7 + - - +
150C VAL* 3.9 6.8 - - + +
193C ILE 4.6 0.4 + - - -
194C LEU* 3.3 47.4 + - + +
196C ASN* 3.1 53.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ARG* 5.7 3.8 - - - +
141C GLN* 2.9 24.4 + - - +
142C MET* 3.4 7.7 + - - +
144C ARG* 1.3 103.7 + - - +
146C ALA* 1.3 57.3 + - - +
147C GLY 3.3 2.4 + - - -
196C ASN 5.5 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ARG* 3.6 33.2 - - + +
114C LEU* 3.5 31.4 - - + +
142C MET 3.1 14.8 + - - +
143C LEU* 3.7 8.5 - - + +
144C ARG 3.1 1.6 - - - -
145C ASP* 1.3 75.6 - - - +
147C GLY* 1.3 58.7 + - - +
148C ALA 3.4 1.1 - - - -
----------------------------------------------------------
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