Contacts of the helix formed by residues 125 - 139 (chain B) in PDB entry 3HUU
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 ASP 125 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASN* 1.3 73.2 - - - +
126B ASN* 1.3 55.7 + - - +
127B ILE* 3.5 10.7 + - - +
128B ASP* 3.1 32.9 + - + +
129B ALA* 2.8 26.8 + - - +
281B LEU* 4.3 23.9 - - + +
282B ILE 4.2 4.6 + - - -
284B THR* 5.0 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ASP* 3.3 29.1 + - - -
124B ASN* 3.0 27.0 + - - +
125B ASP* 1.3 68.9 + - - +
127B ILE* 1.3 65.4 + - - +
129B ALA* 3.7 9.1 - - - +
130B ALA* 3.0 24.8 + - - +
156B VAL* 3.8 19.3 - - - +
159B ASP* 3.6 24.7 + - + +
160B ARG* 2.9 45.4 + - + +
253B ILE* 4.8 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LYS* 5.0 6.3 - - + +
125B ASP* 3.3 8.1 + - - +
126B ASN* 1.3 76.3 - - - +
128B ASP* 1.3 60.1 + - - +
130B ALA 3.3 1.6 + - - -
131B TYR* 2.9 25.1 + - + +
159B ASP* 3.2 43.2 - - + +
162B VAL* 4.2 16.2 - - + -
163B GLY* 3.3 21.0 - - - +
166B GLN* 3.8 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ASP* 3.1 33.4 + - - +
127B ILE* 1.3 79.4 - - - +
129B ALA* 1.3 60.7 + - - +
131B TYR* 3.1 10.9 + - - +
132B GLN* 2.8 61.3 + - - +
284B THR* 5.1 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ASP 2.8 16.6 + - - +
126B ASN* 3.7 15.3 - - - +
128B ASP* 1.3 76.8 - - - +
130B ALA* 1.3 57.7 + - - +
132B GLN* 3.6 5.2 + - - +
133B LEU* 3.1 26.9 + - - +
235B PHE* 4.2 10.7 - - + -
251B VAL* 4.2 18.1 - - + +
253B ILE* 5.5 0.7 - - + -
284B THR* 3.8 30.3 - - + +
286B ILE* 5.7 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASN 3.0 18.2 + - - +
127B ILE 3.7 3.6 - - - +
129B ALA* 1.3 76.2 - - - +
131B TYR* 1.3 66.1 + - - +
133B LEU* 3.3 1.4 + - - +
134B THR* 2.9 29.8 + - - -
147B PHE* 5.3 0.2 - - + -
160B ARG* 3.1 33.0 - - - +
163B GLY 4.3 1.3 - - - -
164B PHE* 3.9 8.3 - - + +
235B PHE* 3.8 20.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
127B ILE 2.9 17.2 + - - +
128B ASP* 3.5 14.8 - - - +
130B ALA* 1.3 76.8 - - - +
132B GLN* 1.3 63.8 + - + +
134B THR* 3.4 2.3 + - - -
135B GLN* 3.0 44.3 + - - +
163B GLY* 3.7 11.8 - - - +
166B GLN* 3.9 19.7 - - + +
167B TYR* 3.4 47.5 - + + -
170B ASP* 2.7 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ASP* 2.8 46.2 + - - +
129B ALA* 3.8 6.5 - - - +
131B TYR* 1.3 75.8 - - + +
133B LEU* 1.3 60.3 + - - +
135B GLN* 3.0 32.8 + - - +
136B TYR* 2.9 29.3 + - - +
284B THR* 6.0 1.3 - - - +
286B ILE* 3.7 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA 3.1 18.1 + - - +
130B ALA* 3.3 5.1 + - - +
132B GLN* 1.3 75.0 - - - +
134B THR* 1.3 65.6 + - - +
136B TYR* 3.2 9.8 + - + +
137B LEU* 3.0 35.2 + - + +
205B ILE* 3.9 17.9 - - + -
233B ALA* 4.3 18.2 - - + -
234B THR 4.1 9.4 - - - +
235B PHE* 3.8 30.1 - - + -
249B THR* 5.0 5.2 - - + -
250B SER 5.2 1.3 - - - -
251B VAL* 3.9 22.0 - - + -
286B ILE* 3.8 24.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ALA 2.9 17.5 + - - -
131B TYR 3.8 3.4 - - - -
133B LEU* 1.3 76.7 - - - +
135B GLN* 1.3 57.7 + - - +
137B LEU* 3.1 11.7 + - - +
138B TYR* 2.8 27.7 + - - +
145B ILE* 3.8 19.9 - - + +
164B PHE* 3.4 39.5 - - + +
167B TYR* 3.5 25.1 - - + -
168B CYS* 4.3 6.7 - - - -
173B ILE* 5.0 0.7 - - + -
205B ILE* 3.9 6.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B TYR* 3.0 31.0 + - + +
132B GLN* 3.0 31.5 + - - +
134B THR* 1.3 76.2 - - - +
136B TYR* 1.3 62.6 + - - +
138B TYR* 3.1 2.6 + - - +
139B HIS* 3.0 51.2 + - + +
167B TYR* 3.4 32.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLN 2.9 13.4 + - - +
133B LEU* 3.4 11.7 - - + +
135B GLN* 1.3 75.7 - - - +
137B LEU* 1.3 76.4 + - + +
139B HIS* 3.3 9.3 + - + +
140B LEU* 3.3 56.6 + - + +
249B THR* 4.1 11.7 - - + -
286B ILE* 3.6 30.5 - - + -
288B GLU* 3.0 34.8 + - + +
292B THR* 3.5 15.8 + - - -
293B THR* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 3.0 21.5 + - + +
134B THR* 3.5 5.4 - - - +
136B TYR* 1.3 85.5 - - + +
138B TYR* 1.3 65.9 + - - +
140B LEU* 3.0 13.9 + - + -
142B HIS* 3.2 36.0 + - + -
145B ILE* 4.1 9.6 - - + -
203B VAL* 4.0 20.9 - - + -
205B ILE* 3.5 39.0 - - + -
233B ALA* 4.5 5.6 - - + -
292B THR* 3.8 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B THR 2.8 7.9 + - - +
135B GLN 3.1 3.8 + - - +
137B LEU* 1.3 76.4 - - - +
139B HIS* 1.3 76.7 + + - +
141B GLY* 2.8 17.2 + - - -
142B HIS* 3.5 13.2 - - - -
143B ARG* 3.0 67.5 + - - -
145B ILE* 4.6 3.5 - - + +
167B TYR* 3.3 35.7 - + + +
171B VAL* 4.0 36.9 + - + +
173B ILE* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLN* 3.0 51.7 + - + +
136B TYR* 3.8 8.5 - - + +
137B LEU 3.2 0.2 - - - -
138B TYR* 1.3 94.6 - + - +
140B LEU* 1.3 59.6 + - - +
141B GLY 3.1 2.2 + - - -
167B TYR* 3.9 5.1 + - - -
294B LYS* 5.8 1.4 + - - +
----------------------------------------------------------
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