Contacts of the helix formed by residues 131 - 141 (chain A) in PDB entry 1X0X
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 131 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 4.8 5.8 - - + +
123A ASP 5.0 0.2 - - - +
129A LEU* 4.4 15.0 - - + -
130A LYS* 1.3 74.4 - - - +
132A ILE* 1.3 60.2 + - - +
133A SER* 4.1 1.8 - - - +
134A GLU* 3.0 30.6 + - + +
135A VAL* 2.9 26.1 + - - +
195A ASP* 2.7 47.3 - - + +
198A GLU* 3.7 35.7 - - + +
199A ILE* 4.1 26.2 - - + -
243A CYS* 5.7 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A HIS* 3.8 17.7 - - + +
98A ILE* 3.2 28.0 - - + -
117A SER* 4.6 1.3 - - - +
119A ILE* 4.0 28.5 - - + +
121A GLY* 3.2 41.3 + - - +
122A VAL* 3.8 4.2 - - - +
123A ASP* 4.0 16.8 - - - +
130A LYS 3.7 0.2 + - - -
131A LEU* 1.3 72.2 - - - +
133A SER* 1.3 58.5 + - - +
135A VAL* 3.1 9.2 + - + +
136A ILE* 2.8 40.5 + - + +
198A GLU* 3.3 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER* 4.3 9.3 + - - -
131A LEU* 4.1 3.6 - - - +
132A ILE* 1.3 77.1 - - - +
134A GLU* 1.3 62.3 + - - +
136A ILE* 3.8 10.3 - - - -
137A GLY* 2.8 26.3 + - - -
144A MET* 3.7 19.2 - - - +
145A SER 4.5 3.6 - - - -
146A VAL* 3.9 16.1 - - - +
194A VAL* 4.7 5.9 - - - +
198A GLU* 2.4 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU 5.0 1.4 - - - +
130A LYS* 4.3 12.8 - - + +
131A LEU* 3.0 39.3 + - + +
133A SER* 1.3 82.4 + - - +
135A VAL* 1.3 65.3 + - - +
137A GLY* 3.7 0.8 - - - -
138A GLU* 2.9 47.2 + - - +
195A ASP* 3.8 19.8 - - - +
244A SER* 5.1 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE* 5.7 6.7 - - + -
99A GLY* 5.8 7.2 - - - +
102A CYS* 5.5 4.0 - - - -
123A ASP* 4.0 24.2 - - - +
130A LYS* 3.8 31.0 - - + +
131A LEU 2.9 19.7 + - - +
132A ILE* 3.4 10.3 - - + +
134A GLU* 1.3 76.9 - - - +
136A ILE* 1.3 66.2 + - + +
138A GLU* 3.3 2.7 + - - +
139A ARG* 3.0 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 3.7 34.1 - - + -
98A ILE* 3.9 27.8 - - + -
102A CYS* 4.1 13.7 - - - -
117A SER* 4.0 21.3 - - - +
119A ILE* 4.2 0.9 - - + -
132A ILE* 2.8 37.0 + - + +
133A SER* 3.8 3.4 - - - +
135A VAL* 1.3 75.6 - - + +
137A GLY* 1.3 64.2 + - - +
140A LEU* 3.2 47.0 + - + +
144A MET* 3.8 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A SER 2.8 22.7 + - - -
134A GLU* 3.3 1.8 + - - -
136A ILE* 1.3 75.5 - - - +
138A GLU* 1.3 57.9 + - - +
141A GLY* 2.9 23.6 + - - -
142A ILE* 3.1 28.3 + - - +
144A MET* 3.7 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LYS* 5.6 0.3 - - - -
130A LYS* 4.5 20.4 + - - -
134A GLU* 2.9 41.8 + - - +
135A VAL* 4.0 3.1 - - - +
137A GLY* 1.3 71.7 - - - +
139A ARG* 1.3 67.7 + - + +
141A GLY* 3.6 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLY* 3.2 20.4 + - - -
102A CYS* 4.1 18.7 + - + +
103A ASP* 3.2 47.5 + - - +
106A LYS* 3.3 54.9 + - - +
135A VAL* 3.0 32.3 + - + +
136A ILE 4.3 0.4 - - - +
138A GLU* 1.3 79.5 - - + +
140A LEU* 1.3 61.1 + - + +
141A GLY 3.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 3.4 37.2 - - + -
102A CYS* 3.8 22.0 - - - +
105A LEU* 3.5 18.2 - - + -
106A LYS* 3.4 33.7 - - - +
107A GLY 5.4 3.0 + - - -
109A LEU* 3.7 23.2 - - + +
136A ILE* 3.2 25.7 + - + +
139A ARG* 1.3 76.3 - - - +
141A GLY* 1.3 65.7 + - - +
142A ILE* 3.5 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA 5.7 0.5 - - - +
137A GLY 2.9 14.9 + - - -
138A GLU* 3.6 5.5 + - - -
139A ARG 3.3 3.8 + - - -
140A LEU* 1.3 78.9 - - - +
142A ILE* 1.3 60.7 + - - +
143A PRO* 4.8 0.3 - - - +
----------------------------------------------------------
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