Contacts of the helix formed by residues 131 - 149 (chain A) in PDB entry 1H7B
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 131 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ALA* 1.3 80.4 - - - +
132A VAL* 1.3 65.3 + - - +
133A ASP* 2.9 14.9 + - - +
134A LYS* 3.0 21.8 + - + +
135A VAL* 2.9 24.1 + - + +
198A THR* 2.8 21.1 + - - -
199A PHE* 4.9 1.6 - - - +
201A THR* 4.1 11.1 + - - +
237A PHE* 3.3 36.6 - - - -
283A VAL* 6.1 1.2 - - - +
284A PRO* 4.9 8.6 + - - +
286A SER* 4.7 1.1 + - - -
307A ASP* 5.3 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 5.0 3.8 - - + -
112A MET* 4.2 13.9 - - + -
129A PHE* 3.8 28.0 - - + +
130A ALA 4.1 1.3 - - - +
131A ASN* 1.3 75.5 - - - +
133A ASP* 1.3 60.3 + - - +
135A VAL* 3.9 7.4 - - - -
136A LEU* 2.9 43.0 + - + +
175A PHE* 4.7 2.0 - - + -
197A ILE* 3.4 39.0 - - + -
198A THR 3.0 6.7 + - - +
199A PHE* 4.4 3.8 - - + -
210A ILE* 3.7 3.5 - - + +
214A ILE* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ASN* 3.3 20.4 + - - +
132A VAL* 1.3 78.7 - - - +
134A LYS* 1.3 68.0 + - - +
137A SER* 3.4 20.6 + - - -
199A PHE* 3.6 12.1 - - + -
200A GLY 2.9 14.1 + - - -
201A THR* 4.8 0.5 + - - -
202A GLY* 3.2 12.7 + - - -
207A GLU* 3.6 28.6 - - - +
210A ILE* 3.5 18.4 - - + +
211A GLN* 2.8 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ASN* 3.0 20.2 + - + +
133A ASP* 1.3 89.2 + - - +
135A VAL* 1.3 65.9 + - + +
137A SER* 3.5 14.0 - - - -
138A PRO* 3.7 5.2 - - - +
201A THR* 3.3 33.3 + - - +
202A GLY* 4.5 2.9 - - - -
207A GLU* 3.1 29.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 4.0 24.2 - - + -
85A LYS* 3.7 50.5 - - + +
88A LEU* 4.9 4.3 - - + -
130A ALA 3.4 16.2 - - - +
131A ASN* 2.9 19.8 + - + +
132A VAL* 4.2 5.6 - - - +
134A LYS* 1.3 78.0 - - + +
136A LEU* 1.3 61.4 + - + +
138A PRO* 3.3 12.3 - - - +
139A TYR* 3.6 10.8 - - + -
307A ASP* 5.1 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 4.7 9.6 - - + -
88A LEU* 3.9 13.7 - - + -
105A ILE* 4.0 7.4 - - + -
108A ALA* 3.8 33.0 - - + +
109A THR* 3.9 10.8 - - + -
112A MET* 4.0 17.3 - - - -
132A VAL* 2.9 22.5 + - + +
135A VAL* 1.3 76.7 - - + +
137A SER* 1.3 64.6 + - - +
138A PRO* 3.3 1.8 - - - -
139A TYR* 2.9 26.1 + - + +
140A VAL* 3.3 9.4 + - - +
175A PHE* 3.5 33.2 - - + -
210A ILE* 3.6 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ASP 3.4 20.5 + - - -
134A LYS 3.5 6.7 - - - -
136A LEU* 1.3 75.6 - - - +
138A PRO* 1.3 69.9 - - - +
140A VAL* 3.0 13.9 + - - +
141A LYS* 3.0 22.8 + - - +
204A ASP* 4.9 0.5 - - - +
206A THR* 2.5 34.3 + - - +
207A GLU* 3.6 14.3 - - - +
210A ILE* 3.7 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 5.7 5.4 - - - +
134A LYS 3.7 6.1 - - - +
135A VAL 3.3 13.7 - - - +
136A LEU 3.3 4.7 - - - -
137A SER* 1.3 95.0 - - - +
139A TYR* 1.3 73.3 + - + +
141A LYS* 3.4 25.9 - - - +
142A ARG* 3.1 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LYS 5.1 0.3 + - - -
88A LEU* 3.4 42.5 + - + +
89A GLU* 3.8 12.3 + - - +
101A THR* 3.6 10.6 - - + +
102A PRO* 3.3 44.0 - - + -
104A SER 3.9 3.1 - - - +
105A ILE* 3.5 33.9 + - + -
108A ALA* 3.9 7.0 - - + -
135A VAL* 3.6 16.4 - - + -
136A LEU* 2.9 30.4 + - + +
138A PRO* 1.3 87.5 - - + +
140A VAL* 1.3 64.9 + - - +
141A LYS 3.2 0.4 - - - -
142A ARG* 3.4 15.4 + - - +
143A THR* 3.1 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 3.5 28.0 - - + -
136A LEU 3.3 1.8 + - - +
137A SER* 3.0 8.4 + - - +
139A TYR* 1.3 77.8 - - - +
141A LYS* 1.3 64.5 + - - +
143A THR* 3.2 5.3 + - - -
144A TYR* 3.1 20.3 + - - +
167A THR* 4.0 3.8 - - + +
171A VAL* 3.8 15.3 - - + -
205A TRP* 4.3 0.2 - - + -
206A THR* 3.4 19.3 - - + +
209A MET* 3.1 34.5 - - + -
210A ILE* 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A SER* 3.0 19.0 + - - +
138A PRO* 3.4 35.3 - - - +
140A VAL* 1.3 77.0 - - - +
142A ARG* 1.3 63.5 + - - +
144A TYR* 3.0 10.8 + - - +
145A ALA* 2.9 21.4 + - - +
204A ASP* 5.4 4.7 + - - +
205A TRP* 4.8 9.0 - - + +
206A THR* 4.0 17.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A THR* 3.2 32.2 - - - +
102A PRO 3.6 12.4 + - - -
103A LYS* 3.2 40.8 - - + +
138A PRO* 3.1 27.5 + - - +
139A TYR* 3.5 15.4 - - - +
140A VAL 3.2 0.2 - - - -
141A LYS* 1.3 79.9 - - - +
143A THR* 1.3 62.2 + - - +
145A ALA* 3.1 18.8 + - + +
146A LYS* 3.2 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LYS 4.9 2.2 - - - -
104A SER* 3.7 9.7 + - - +
105A ILE* 3.1 35.2 + - + +
139A TYR 3.1 5.5 + - - -
140A VAL* 3.2 7.6 + - - -
142A ARG* 1.3 79.4 - - - +
144A TYR* 1.3 62.2 + - - +
146A LYS* 3.3 9.0 + - - +
147A HIS* 3.1 40.0 + - + +
167A THR* 3.9 12.1 - - + +
170A ASP* 3.3 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A VAL 3.1 12.0 + - - +
141A LYS* 3.0 11.6 + - - +
143A THR* 1.3 73.5 - - - +
145A ALA* 1.3 68.5 + - - +
146A LYS 3.0 2.0 - - - -
147A HIS* 2.9 13.7 + - - +
148A ILE* 3.1 29.5 + - + +
160A LEU* 3.6 22.5 + - - +
163A ALA* 3.1 28.0 - - + +
164A GLN* 3.5 20.8 + - + +
167A THR* 3.1 27.4 - - - +
205A TRP* 3.9 29.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LYS 2.9 11.0 + - - +
142A ARG* 3.1 12.3 + - + +
144A TYR* 1.3 78.6 - - - +
146A LYS* 1.3 57.3 + - - +
148A ILE* 3.6 7.3 + - - +
149A GLU* 3.1 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LYS* 4.2 36.7 + - - +
104A SER* 5.3 7.3 - - - -
142A ARG 3.2 9.6 + - - +
143A THR* 3.6 11.7 - - - +
144A TYR 3.0 1.0 - - - -
145A ALA* 1.3 76.5 - - - +
147A HIS* 1.3 63.3 + - + +
148A ILE 3.2 0.4 - - - -
149A GLU* 4.0 18.1 - - - +
150A ASP* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A THR* 3.1 31.4 + - + +
144A TYR 2.9 6.5 + - - +
146A LYS* 1.3 78.6 + - + +
148A ILE* 1.3 61.1 + - - +
150A ASP* 3.8 6.8 + - - +
151A ALA* 3.1 23.6 + - - +
162A TYR* 3.4 16.7 + - + -
163A ALA* 3.9 18.2 - - + -
166A LYS* 3.3 40.1 - - + +
167A THR* 3.6 8.3 - - - +
170A ASP* 3.1 31.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TYR* 3.1 36.6 + - + +
145A ALA* 3.9 7.6 - - - +
147A HIS* 1.3 77.3 - - - +
149A GLU* 1.3 59.4 + - + +
150A ASP 2.8 4.7 + - - -
151A ALA* 2.9 20.8 + - + +
152A GLU* 3.3 13.3 + - - +
159A ALA* 4.2 15.9 - - + +
160A LEU* 4.3 14.8 - - + -
163A ALA* 3.4 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ALA 3.1 18.0 + - - +
146A LYS* 3.8 19.1 + - - +
148A ILE* 1.3 78.7 - - + +
150A ASP* 1.3 59.9 + - - +
152A GLU* 3.9 14.3 - - + +
153A LYS* 3.3 20.8 + - + +
----------------------------------------------------------
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