Contacts of the strand formed by residues 136 - 144 (chain A) in PDB entry 4JXJ
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 VAL 136 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 3.6 31.0 - - + -
110A LYS* 4.8 1.3 - - - -
111A ILE* 3.4 7.4 - - + +
113A ILE* 4.2 10.8 - - + -
129A TRP 4.4 0.4 - - - +
132A GLU 3.8 8.1 - - - +
133A SER* 2.9 23.5 + - - +
134A SER 3.3 2.2 - - - +
135A LEU* 1.3 78.8 - - - +
137A ALA* 1.3 65.5 + - - +
138A SER* 3.5 29.8 - - - +
139A MET* 3.8 22.4 - - + -
199A PRO* 3.7 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LYS* 4.0 17.2 - - + +
111A ILE 2.7 19.0 + - - +
112A THR* 3.7 16.2 - - - +
136A VAL* 1.3 75.3 - - - +
138A SER* 1.3 64.1 + - - +
198A THR* 4.1 8.1 - - - +
199A PRO* 3.6 11.6 - - - +
303A IOD 4.5 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A SER 4.3 11.6 + - - -
112A THR* 3.5 17.7 + - - +
113A ILE 3.0 23.8 + - - -
136A VAL* 3.5 7.7 - - - +
137A ALA* 1.3 82.3 - - - +
139A MET* 1.3 69.9 + - - +
140A THR* 4.8 1.6 + - - -
196A LYS* 4.7 7.9 - - - +
197A LEU 3.6 11.4 - - - -
198A THR* 4.1 12.8 - - - -
199A PRO* 4.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 3.2 18.2 - - + +
126A VAL* 5.1 3.1 - - - +
129A TRP* 3.6 45.3 - - + +
130A LEU* 3.6 34.8 - - + -
133A SER* 5.5 1.3 - - - -
136A VAL* 3.8 22.0 - - + -
138A SER* 1.3 79.0 - - - +
140A THR* 1.3 61.7 + - - +
141A LEU* 4.0 23.6 - - + -
195A VAL 3.8 0.8 - - - +
196A LYS* 3.2 6.5 - - - +
197A LEU* 2.7 51.0 + - + +
199A PRO* 5.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ILE* 3.8 30.9 - - + +
37A ALA* 4.6 2.7 - - + -
38A SER* 3.1 34.8 + - - +
112A THR* 6.0 0.3 - - - +
113A ILE 2.8 9.3 + - - +
114A ILE* 3.3 7.1 - - - +
115A SER 3.1 22.7 + - - -
138A SER* 4.8 2.1 + - - -
139A MET* 1.3 69.0 - - - +
141A LEU* 1.3 60.8 + - - +
176A CYS* 5.5 0.2 - - - -
194A ILE* 3.8 22.4 - - + -
195A VAL 3.4 4.3 - - - +
196A LYS* 3.5 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ILE* 6.1 0.7 - - - -
113A ILE* 4.0 26.5 - - + -
115A SER* 3.1 15.0 - - - +
117A LEU* 4.3 9.9 - - + -
126A VAL* 3.6 31.2 - - + -
129A TRP* 4.0 11.2 - - + -
139A MET* 4.0 22.0 - - + -
140A THR* 1.3 85.5 - - - +
142A MET* 1.3 60.4 + - - +
143A LEU* 4.0 9.4 - - + -
193A ALA 3.5 1.4 - - - +
194A ILE* 3.2 6.7 - - - -
195A VAL* 2.8 46.2 + - + +
197A LEU* 4.0 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 4.2 15.3 - - + -
30A LEU* 5.2 0.2 - - - -
34A ILE* 3.8 23.7 - - + +
56A LEU* 5.4 2.9 - - + -
115A SER 2.8 9.6 + - - +
116A ASN* 3.4 37.6 - - + +
117A LEU 3.1 25.3 + - - +
141A LEU* 1.3 72.5 - - - +
143A LEU* 1.3 65.0 + - - +
179A VAL* 3.9 17.3 - - - -
184A PHE* 3.8 27.8 - - + -
192A SER* 3.9 16.2 - - - +
193A ALA 3.2 4.9 - - - +
194A ILE* 3.3 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN* 5.3 0.2 - - - -
117A LEU* 3.1 45.8 - - + -
122A GLY* 4.3 3.6 - - - -
126A VAL* 4.5 6.5 - - + -
141A LEU* 4.3 7.6 - - + -
142A MET* 1.3 74.5 - - - +
144A GLN* 1.3 70.0 + - - +
147A VAL* 4.5 6.1 - - + -
148A VAL* 3.8 6.6 - - + +
151A ILE* 3.6 23.6 - - + -
192A SER* 3.0 8.7 - - - -
193A ALA* 2.6 38.3 + - - +
195A VAL* 3.5 31.0 - - + -
304A IOD 4.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A TYR* 4.0 24.3 - - + +
143A LEU* 1.3 74.7 - - - +
145A LYS* 1.3 60.3 + - - +
146A GLU* 3.2 11.5 - - + +
147A VAL* 3.0 36.0 + - + +
148A VAL* 3.1 9.7 + - - +
190A VAL* 3.4 30.4 - - + +
191A TYR 3.5 8.7 - - - +
192A SER* 4.1 4.4 + - - +
304A IOD 3.9 15.5 - - + +
----------------------------------------------------------
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