Contacts of the helix formed by residues 135 - 149 (chain A) in PDB entry 3HVK
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 GLU* 2.9 16.0 + - - +
134A MET* 1.3 78.5 - - + +
136A PRO* 1.3 66.8 - - - +
137A ASP* 2.9 25.6 + - - +
138A TYR* 3.1 39.7 + - + -
139A ALA* 2.8 27.2 + - - +
159A ASN* 3.9 0.4 - - - -
267A 719 3.6 9.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A MET 3.4 9.8 - - - +
135A ASN* 1.3 87.4 - - - +
137A ASP* 1.3 67.7 + - - +
139A ALA* 3.7 1.4 - - - +
140A ALA* 3.0 24.1 + - - +
159A ASN* 3.5 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ASN* 2.9 13.5 + - - +
136A PRO* 1.3 83.7 - - - +
138A TYR* 1.3 67.3 + - + +
140A ALA* 3.4 7.0 + - - +
141A ILE* 3.0 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 5.8 1.1 - - + -
49A GLU* 3.5 49.5 + - + -
83A MET* 5.1 2.8 - - + +
111A TYR* 3.1 40.8 - + - +
112A CYS* 5.6 0.2 - - - -
133A GLU* 3.8 7.9 - - - -
135A ASN* 3.1 38.2 + - + +
137A ASP* 1.3 82.0 - - + +
139A ALA* 1.3 60.5 + - - +
141A ILE* 3.2 6.1 + - + +
142A THR* 2.9 26.2 + - - -
267A 719 3.3 27.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU* 3.5 19.2 - - + +
135A ASN 2.8 15.6 + - - +
136A PRO 3.7 4.7 - - - +
137A ASP 3.3 0.2 - - - -
138A TYR* 1.3 77.4 - - - +
140A ALA* 1.3 56.4 + - - +
142A THR* 3.3 3.9 + - - -
143A GLN* 2.9 28.8 + - - +
157A ILE* 3.9 16.4 - - + +
159A ASN* 4.0 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PRO 3.0 15.6 + - - +
137A ASP* 3.7 6.7 - - - +
139A ALA* 1.3 74.3 - - - +
141A ILE* 1.3 64.8 + - + +
143A GLN* 3.4 5.7 + - - +
144A GLN* 3.1 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 4.8 1.8 - - - +
49A GLU* 3.4 44.2 - - + +
50A GLN* 3.8 20.6 - - + +
53A LEU* 4.3 18.2 - - + +
112A CYS* 4.0 30.3 - - + +
137A ASP* 3.0 23.6 + - + +
138A TYR* 3.2 12.3 + - + +
140A ALA* 1.3 75.1 - - + +
142A THR* 1.3 59.6 + - - +
144A GLN* 3.2 9.8 + - - +
145A MET* 2.8 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ALA* 3.5 20.1 - - + +
111A TYR 2.8 27.0 + - - -
112A CYS 3.7 8.5 - - - -
113A GLY* 3.2 24.3 + - - -
116A ALA* 4.9 0.4 - - + -
131A THR* 4.5 2.7 - - + -
138A TYR 2.9 11.5 + - - -
139A ALA* 3.6 7.0 - - - -
141A ILE* 1.3 78.5 - - - +
143A GLN* 1.3 62.8 + - - +
145A MET* 3.2 2.3 + - - +
146A LEU* 3.0 31.0 + - + +
157A ILE* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ALA 2.9 17.1 + - - +
140A ALA* 3.8 7.2 - - - +
142A THR* 1.3 75.4 - - - +
144A GLN* 1.3 59.4 + - + +
146A LEU* 3.3 2.1 + - - +
147A ASN* 2.9 64.2 + - - +
152A GLN* 4.2 11.3 + - - +
155A VAL 5.4 0.6 + - - -
157A ILE* 3.3 40.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
50A GLN* 5.4 3.1 + - - +
53A LEU* 3.7 32.3 - - + +
57A GLN* 4.4 11.5 + - - +
140A ALA* 3.1 34.8 + - + +
141A ILE* 3.7 5.9 - - - +
143A GLN* 1.3 79.0 - - + +
145A MET* 1.3 57.4 + - - +
147A ASN* 3.6 12.4 - - - +
148A PHE* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 4.5 4.9 - - + -
53A LEU* 3.9 27.9 - - + +
56A VAL* 3.9 25.1 - - + -
68A VAL* 3.9 21.7 - - + +
72A ILE* 3.9 20.4 - - + -
112A CYS* 3.4 29.6 - - + +
113A GLY* 4.7 3.6 - - - -
117A VAL* 4.2 18.2 - - + -
141A ILE* 2.8 21.0 + - + +
142A THR* 3.5 4.0 - - - +
144A GLN* 1.3 76.2 - - - +
146A LEU* 1.3 57.3 + - - +
148A PHE* 3.3 5.3 + - - +
149A ALA* 3.0 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLY 5.1 0.9 - - - +
116A ALA* 4.1 9.0 - - + +
117A VAL* 3.8 33.7 - - + +
142A THR* 3.0 25.8 + - + +
143A GLN* 3.8 3.8 - - - +
145A MET* 1.3 72.2 - - + +
147A ASN* 1.3 66.8 + - - +
149A ALA* 3.3 3.4 + - - -
150A GLY 3.1 3.5 + - - -
151A LEU* 2.9 47.8 + - + -
152A GLN* 4.3 11.0 - - - +
155A VAL* 3.6 26.5 - - + -
157A ILE* 3.5 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLN* 2.9 51.7 + - - +
144A GLN* 3.6 12.2 - - - +
146A LEU* 1.3 76.3 - - - +
148A PHE* 1.3 62.3 + - - +
150A GLY* 3.0 12.0 + - - -
152A GLN* 3.2 28.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 5.9 2.0 - - + -
56A VAL* 4.3 12.6 - - + -
57A GLN* 4.3 32.1 - - + +
60A ALA* 3.4 28.7 - - + -
61A LYS 3.1 23.8 - - - -
62A PRO* 3.0 42.6 - - + +
63A GLY 2.8 23.7 + - - -
68A VAL* 3.6 15.9 - - + -
144A GLN 2.9 17.6 + - - +
145A MET* 3.6 6.7 - - - +
146A LEU 3.3 0.2 - - - -
147A ASN* 1.3 77.7 - - - +
149A ALA* 1.3 57.3 + - - +
150A GLY* 3.2 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLY* 3.4 22.4 - - - +
64A ASP 4.6 1.6 - - - +
65A PRO* 3.6 18.9 - - + +
68A VAL* 4.2 20.2 - - + -
117A VAL* 4.3 10.1 - - + -
145A MET 3.0 17.1 + - - +
146A LEU 3.7 5.2 - - - +
147A ASN 3.2 0.2 - - - -
148A PHE* 1.3 77.4 - - - +
150A GLY* 1.3 59.4 + - - +
151A LEU* 3.6 21.9 + - + -
----------------------------------------------------------
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