Contacts of the helix formed by residues 135 - 146 (chain A) in PDB entry 4YXH
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 135 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PHE 3.4 0.8 + - - -
134A GLY* 1.3 78.5 - - - +
136A ASP* 1.3 62.0 + - - +
137A TYR* 3.9 0.7 - - - +
138A GLU* 2.8 43.4 + - - +
139A ASP* 3.1 21.8 + - - +
104H TYR* 3.5 10.2 - - - -
91L SER 3.1 20.9 - - - +
92L ASN 3.1 15.9 - - - +
93L THR* 3.8 4.4 - - - +
94L TRP* 3.1 48.7 - - - +
96L TYR* 4.4 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ASN* 1.3 71.6 - - - +
137A TYR* 1.3 58.3 + - - +
139A ASP* 3.8 4.4 - - - +
140A ARG* 3.0 31.6 + - - +
143A ARG* 5.5 0.2 + - - -
102H GLY 4.8 2.9 - - - +
103H TYR* 4.9 1.9 - - - -
104H TYR* 3.9 8.1 - - - -
32L SER* 2.6 36.9 + - - +
50L TYR* 2.5 31.1 + - - -
91L SER* 3.1 20.3 + - - +
92L ASN* 4.1 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ASN* 3.9 0.2 - - - +
136A ASP* 1.3 78.1 - - - +
138A GLU* 1.3 70.9 + - + +
140A ARG* 3.3 7.7 + - + +
141A TYR* 2.7 65.1 + + + +
193A THR* 5.6 7.9 - - + -
92L ASN* 3.1 29.0 + - - +
93L THR* 3.8 18.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
133A PHE* 3.6 28.1 - - + +
135A ASN* 2.8 29.1 + - - +
137A TYR* 1.3 84.0 - - + +
139A ASP* 1.3 58.9 + - - +
141A TYR* 4.1 1.8 - - - -
142A TYR* 2.8 33.3 + - - +
193A THR* 5.0 4.9 - - + -
196A LYS* 3.1 37.9 + - - -
197A MET* 3.5 21.1 - - + +
57H TYR* 4.5 0.3 + - - -
93L THR* 6.0 1.4 - - + +
94L TRP* 3.2 22.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ILE 4.4 2.4 - - - +
132A HIS* 3.4 17.7 + - - -
133A PHE* 2.5 35.9 + - - +
134A GLY 3.5 1.2 + - - -
135A ASN 3.1 17.2 + - - +
136A ASP* 3.8 4.5 - - - +
138A GLU* 1.3 74.9 - - - +
140A ARG* 1.3 65.1 + - - +
142A TYR* 3.4 5.5 + - - +
143A ARG* 3.0 38.4 + - - +
102H GLY* 3.7 7.5 - - - +
104H TYR* 2.3 33.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ASP 3.0 18.2 + - - +
137A TYR* 3.7 7.9 - - + +
139A ASP* 1.3 77.6 - - - +
141A TYR* 1.3 62.2 + - - +
143A ARG* 3.2 31.4 + - - +
144A GLU* 3.0 58.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TYR* 2.7 53.1 + + + +
138A GLU* 3.7 6.7 - - - +
140A ARG* 1.3 71.4 - - - +
142A TYR* 1.3 57.9 + - - +
144A GLU* 3.1 7.0 + - - -
145A ASN* 2.8 64.2 + - + +
148A ARG* 3.6 2.4 + - - -
149A TYR* 3.2 22.4 - - - -
191A THR* 3.6 11.6 - - + +
193A THR* 4.2 10.3 - - + -
194A ASP* 2.4 29.9 + - - -
197A MET* 3.4 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ARG* 5.1 0.3 - - - +
129A PRO* 3.3 16.0 + - - +
130A LEU* 5.2 3.8 - - + -
131A ILE* 3.8 44.6 - - + +
133A PHE* 3.5 32.5 - + + -
138A GLU 2.8 21.5 + - - +
139A ASP* 3.6 4.3 - - - +
141A TYR* 1.3 76.1 - - - +
143A ARG* 1.3 67.2 + - + +
145A ASN* 5.0 0.4 - - - -
146A MET* 2.9 70.7 + - + +
149A TYR* 4.0 23.3 - + - -
197A MET* 4.2 11.4 - - + -
201A VAL* 4.0 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ASP* 3.0 35.4 + - - +
140A ARG* 3.2 38.2 + - - +
142A TYR* 1.3 78.2 - - + +
144A GLU* 1.3 65.2 + - + +
146A MET* 3.5 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 3.0 59.4 + - + +
141A TYR* 4.7 4.9 - - - -
142A TYR 3.1 0.2 - - - -
143A ARG* 1.3 84.6 - - + +
145A ASN* 1.3 72.9 + - - +
146A MET 3.5 0.2 - - - -
147A TYR* 3.2 24.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TYR* 2.8 61.0 + - + +
142A TYR 4.6 0.2 - - - +
144A GLU* 1.3 87.7 + - - +
146A MET* 1.3 65.1 + - - +
147A TYR* 3.1 8.6 - - - -
148A ARG* 2.7 51.2 + - - +
149A TYR* 3.6 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ARG* 2.5 64.4 + - + +
129A PRO 4.0 6.3 - - - +
130A LEU* 5.7 2.9 - - - -
142A TYR* 2.9 64.0 + - + +
143A ARG* 3.5 20.4 - - - +
144A GLU 3.5 0.8 - - - -
145A ASN* 1.3 76.8 - - - +
147A TYR* 1.3 55.0 + - + +
148A ARG 3.0 2.7 + - - -
149A TYR* 3.2 20.1 + - + +
----------------------------------------------------------
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