Contacts of the helix formed by residues 131 - 143 (chain A) in PDB entry 4X61
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 ASN 131 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ARG* 5.3 2.9 + - - -
93A ASP* 3.1 11.8 - - - +
125A PRO 4.9 1.7 - - - +
126A LEU* 3.3 33.8 - - - +
127A ASN* 4.5 1.3 + - - +
128A GLN* 3.2 34.8 + - - +
129A GLU 3.4 6.2 + - - +
130A ASP* 1.3 82.2 + - - +
132A THR* 1.3 58.9 + - - +
134A LEU* 3.2 13.9 + - + +
135A ALA* 2.9 30.9 + - - +
188A TRP* 5.0 6.6 + - - +
192A PHE* 4.1 18.2 - - + -
195A LEU* 4.8 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASP* 3.5 1.5 + - - -
130A ASP* 2.6 24.4 + - - -
131A ASN* 1.3 77.9 + - - +
133A ASN* 1.3 58.3 + - - +
135A ALA* 3.4 3.5 + - - +
136A ARG* 3.1 24.6 + - - +
195A LEU* 3.9 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PRO* 3.0 25.4 + - - +
93A ASP* 2.9 18.7 + - - +
100A ARG* 3.9 8.5 - - + +
104A GLU* 3.0 35.4 + - - +
132A THR* 1.3 75.1 - - - +
134A LEU* 1.3 60.1 + - - +
136A ARG* 2.7 31.3 + - - +
137A VAL* 2.9 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 4.5 10.3 - - + -
91A ARG* 5.5 4.5 - - - +
92A PRO* 3.6 34.4 - - + +
93A ASP* 3.2 14.3 + - - +
107A MET* 3.4 30.6 - - + +
124A LEU* 4.4 8.5 - - + -
125A PRO* 3.9 22.4 - - + +
126A LEU* 4.3 0.9 - - + -
131A ASN* 3.2 20.6 + - + +
133A ASN* 1.3 75.5 - - - +
135A ALA* 1.3 58.1 + - - +
138A LEU* 2.9 25.6 + - - +
153A MET* 4.2 8.3 - - + -
192A PHE* 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ASN 2.9 17.2 + - - +
132A THR 3.5 4.9 - - - +
134A LEU* 1.3 75.2 - - - +
136A ARG* 1.3 56.2 + - - +
138A LEU* 3.4 1.2 + - - +
139A THR* 2.7 38.4 + - - -
192A PHE* 3.4 27.8 - - + -
195A LEU* 3.9 24.2 - - + -
196A CYS* 3.9 11.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU* 3.7 22.6 + - - +
108A LEU* 6.4 0.2 - - - +
132A THR 3.1 14.0 + - - +
133A ASN* 2.7 48.5 + - - +
135A ALA* 1.3 75.4 - - - +
137A VAL* 1.3 70.9 + - - +
139A THR* 3.1 6.6 + - - -
140A ASN* 2.8 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PRO* 5.0 1.6 - - + -
104A GLU* 4.0 33.7 - - + +
107A MET* 3.7 30.7 - - + -
108A LEU* 3.9 31.2 - - + +
111A LEU* 5.4 0.4 - - + -
133A ASN* 2.9 22.3 + - - +
136A ARG* 1.3 93.9 - - - +
138A LEU* 1.3 63.1 + - - +
140A ASN* 3.5 6.7 + - - +
141A HIS* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A MET* 3.6 12.0 - - + +
111A LEU* 4.1 12.8 - - + -
124A LEU* 4.8 7.4 - - + -
134A LEU 2.9 19.3 + - - +
135A ALA* 3.7 4.0 - - - +
137A VAL* 1.3 75.7 - - - +
139A THR* 1.3 63.5 + - - +
141A HIS* 2.9 17.9 + - + +
142A ILE* 3.0 23.1 + - + +
151A PHE* 4.0 39.7 - - + -
153A MET* 4.4 10.3 - - - -
192A PHE* 3.5 31.2 - - + -
196A CYS* 4.5 0.4 - - - -
202A ILE* 3.9 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ALA 2.7 29.1 + - - -
136A ARG* 3.5 5.4 - - - -
138A LEU* 1.3 71.4 - - - +
140A ASN* 1.3 68.1 + - - +
142A ILE* 2.9 21.2 + - + +
143A HIS* 2.9 43.3 + - + +
195A LEU 4.4 5.2 + - - +
196A CYS* 3.4 33.3 - - + +
197A ASP* 6.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 5.4 4.3 - - + -
136A ARG* 2.8 56.9 + - - +
137A VAL* 3.8 5.4 - - - +
139A THR* 1.3 77.1 - - - +
141A HIS* 1.3 60.9 + - - +
143A HIS* 3.2 13.5 + - - +
144A THR* 2.9 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 4.2 13.8 - - + +
111A LEU* 3.6 49.3 + - + +
112A ASN* 3.4 27.5 + - - -
115A ALA* 4.5 4.8 - - + +
137A VAL 3.1 12.6 + - - +
138A LEU* 2.9 11.3 + - + +
140A ASN* 1.3 75.7 - - - +
142A ILE* 1.3 63.1 + - - +
144A THR* 3.1 28.0 + - - +
147A HIS* 3.3 30.3 + + - -
149A SER* 6.1 0.2 - - - -
151A PHE* 3.6 29.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 3.0 25.7 + - + +
139A THR* 2.9 16.2 + - + +
141A HIS* 1.3 77.9 - - - +
143A HIS* 1.3 70.9 + - + +
144A THR 3.3 3.0 + - - -
145A GLY 4.4 3.8 - - - +
147A HIS* 4.1 8.6 + - - -
151A PHE* 4.0 23.6 - - + -
196A CYS* 5.8 0.2 - - + -
199A SER* 3.9 17.0 - - - +
201A ARG* 4.1 27.7 + - + +
202A ILE* 3.8 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A THR* 2.9 43.9 + - + +
140A ASN* 3.2 7.3 + - - +
141A HIS 3.2 0.8 - - - -
142A ILE* 1.3 89.4 - - + +
144A THR* 1.3 61.1 + - - +
145A GLY 4.3 1.8 - - - -
196A CYS 6.0 1.3 - - - -
----------------------------------------------------------
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