Contacts of the helix formed by residues 129 - 139 (chain B) in PDB entry 4B94
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 ARG 129 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASP 3.0 31.5 + - - -
127B ASP* 3.8 4.8 - - - +
128B ALA* 1.3 75.8 - - - +
130B ASP* 1.4 71.7 - - - +
131B TYR 3.3 0.3 + - - -
132B PHE* 3.3 7.2 + - - +
133B GLN* 3.2 23.5 + - - +
149B PHE* 4.6 5.5 - - + -
152B PHE* 3.9 26.6 - - + -
153B GLU* 5.4 3.6 - - - +
100D PRO* 3.6 19.0 + - + +
101D ASP* 3.0 20.6 + - - +
134D MET* 6.4 0.2 - - - -
137D ALA* 5.4 4.3 + - - +
138D ASN* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASP 5.2 0.2 + - - -
128B ALA 3.4 1.2 - - - -
129B ARG* 1.4 84.3 - - - +
131B TYR* 1.3 66.8 + - + +
133B GLN* 3.3 9.0 + - - +
134B MET* 2.8 32.3 + - - +
95D ILE* 3.8 22.6 - - + +
98D LEU 4.7 1.0 - - - +
100D PRO* 3.6 26.0 - - + +
109D PHE* 3.9 10.2 - - - -
113D GLN* 4.0 1.2 - - - +
134D MET* 3.6 16.3 - - - +
138D ASN* 2.9 32.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLN 4.5 0.9 - - - +
116B PHE* 3.6 11.0 - + + -
117B ALA* 3.7 22.9 - - + +
120B LYS* 3.6 43.6 + - + +
127B ASP* 3.5 20.2 + - - -
128B ALA* 3.1 21.6 + - - +
130B ASP* 1.3 81.1 - - + +
132B PHE* 1.3 58.2 + - - +
134B MET 3.6 0.3 + - - -
135B ALA* 3.1 26.9 + - - +
95D ILE 3.8 12.3 - - - -
96D GLU* 3.3 48.7 + - - +
98D LEU 5.0 1.6 - - - -
99D PRO* 3.5 34.7 - - - +
100D PRO* 4.6 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B VAL* 4.8 1.6 - - + -
117B ALA* 3.5 41.7 - - + -
118B GLU* 3.8 11.9 - - + -
121B ALA* 4.0 8.5 - - + -
128B ALA 3.5 15.0 - - - -
129B ARG 3.3 5.6 + - - +
131B TYR* 1.3 73.0 - - - +
133B GLN* 1.3 60.9 + - - +
135B ALA* 3.3 6.6 + - + +
136B ARG* 2.9 30.7 + - - +
145B VAL* 5.3 0.8 - - - +
148B SER* 3.5 30.1 - - - -
149B PHE* 3.5 46.8 - + + +
152B PHE* 3.5 39.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG* 3.2 13.3 + - - +
130B ASP 3.3 9.9 - - - +
132B PHE* 1.3 78.1 - - - +
134B MET* 1.3 58.0 + - + +
136B ARG* 3.4 19.3 + - - +
137B ALA* 3.0 28.2 + - - +
149B PHE* 3.5 32.4 - - - -
161B LYS* 5.5 3.0 + - - +
130D ASP* 4.1 13.0 + - - +
131D TYR* 3.7 21.1 + - + -
134D MET* 3.4 43.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLN* 3.7 2.2 - - - -
130B ASP 2.8 16.0 + - - +
131B TYR 3.9 0.2 - - - +
133B GLN* 1.3 82.8 - - + +
135B ALA* 1.4 59.1 + - - +
137B ALA* 3.3 1.6 + - - +
138B ASN* 3.0 40.6 + - - +
92D SER* 3.7 36.1 - - - +
95D ILE* 3.6 24.0 - - + -
96D GLU* 3.4 30.1 - - + +
116D PHE* 3.7 31.0 - - + -
131D TYR* 4.3 0.7 - - + -
134D MET* 3.9 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLN* 3.4 40.1 + - + +
114B VAL* 4.2 7.6 - - + +
117B ALA* 5.2 0.7 - - + -
131B TYR 3.1 18.1 + - - +
132B PHE* 3.3 9.2 + - + +
134B MET* 1.4 74.1 - - - +
136B ARG* 1.3 58.5 + - - +
139B CYS* 2.9 35.6 + - - +
145B VAL* 3.4 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PHE 2.9 16.2 + - - +
133B GLN* 3.6 20.1 + - - +
135B ALA* 1.3 76.4 - - - +
137B ALA* 1.4 61.4 + - - +
140B LYS* 3.1 30.1 + - - +
145B VAL* 3.7 11.8 - - + +
146B HIS* 3.4 41.6 + - + +
149B PHE* 3.9 19.9 - - + -
161B LYS* 5.0 0.2 - - - +
165B LEU* 3.5 25.8 - - - +
168B LYS* 3.6 18.2 - - - +
1199B MLI 3.2 36.7 + - + +
127D ASP 5.7 0.2 + - - -
130D ASP* 2.6 32.5 + - - +
131D TYR* 4.4 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLN 3.0 14.3 + - - +
134B MET* 3.3 7.4 + - - +
136B ARG* 1.4 76.7 - - - +
138B ASN* 1.3 63.8 + - - +
140B LYS* 4.7 9.7 + - - +
1198B GOL 3.3 17.7 + - - -
1199B MLI 3.7 6.8 - - - +
116D PHE* 4.1 21.1 - - + -
120D LYS* 3.7 8.6 + - - -
131D TYR* 3.2 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PRO* 3.5 14.5 - - + +
104B GLY* 3.5 25.5 - - - +
109B PHE* 4.0 8.7 - - + -
113B GLN* 2.9 33.7 + - - +
134B MET* 3.0 18.0 + - - +
137B ALA* 1.3 79.2 - - - +
139B CYS* 1.3 65.1 + - - +
140B LYS* 3.8 2.0 - - - -
1198B GOL 2.6 31.9 + - - +
88D ILE* 5.7 0.2 - - - +
92D SER* 3.2 31.2 + - - -
96D GLU* 5.2 0.4 + - - +
116D PHE* 5.7 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TYR 5.4 0.9 - - - -
104B GLY 4.2 9.0 - - - +
106B ASN 5.5 0.2 - - - -
109B PHE* 3.7 23.1 - - - -
110B ALA* 3.6 39.0 - - + -
113B GLN* 3.9 11.0 - - - -
135B ALA* 2.9 18.8 + - - +
136B ARG 3.9 1.6 - - - -
138B ASN* 1.3 85.5 - - - +
140B LYS* 1.3 64.1 + - - +
141B LYS 3.0 4.6 + - - -
142B PHE* 3.2 14.8 + - + +
145B VAL* 3.6 18.0 - - + +
----------------------------------------------------------
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