Contacts of the helix formed by residues 138 - 153 (chain A) in PDB entry 2A8I
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 138 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 3.5 27.3 + - + +
94A GLU* 3.0 20.4 + - - +
95A ASP* 2.9 24.8 + - - +
136A ILE* 3.9 12.6 - - - +
137A LYS* 1.3 98.3 + - - +
139A PRO* 1.3 67.0 - - - +
140A VAL 3.2 1.6 - - - -
141A SER* 3.0 33.5 + - - +
142A VAL 3.7 1.9 + - - -
179A ILE* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 3.4 13.9 - - - +
102A GLY* 4.1 6.3 - - - -
115A CYS* 3.4 36.6 - - + -
117A ALA* 3.7 19.7 - - + +
130A VAL* 3.9 8.1 - - + +
133A LEU* 4.0 23.8 - - + -
136A ILE* 3.9 8.3 - - - +
137A LYS 3.2 13.2 - - - +
138A ASN* 1.3 83.4 - - - +
140A VAL* 1.3 61.8 + - - +
142A VAL* 3.0 16.2 + - + +
143A ALA* 3.1 9.0 + - - +
251A SER* 4.2 1.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
87A THR* 4.2 15.7 - - + +
90A LEU* 3.8 35.0 - - + -
91A VAL* 3.9 17.9 - - + -
94A GLU* 3.1 33.5 + - - +
117A ALA* 3.8 10.9 - - + +
118A SER 5.0 5.6 - - - +
119A ILE* 5.1 4.7 - - + -
139A PRO* 1.3 76.8 - - - +
141A SER* 1.3 61.3 + - - +
143A ALA* 3.2 3.7 + - + +
144A ASN* 2.8 28.5 + - - +
249A ALA* 4.4 13.2 - - + -
250A VAL 5.5 0.2 - - - +
251A SER* 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A THR* 4.5 6.0 - - - +
91A VAL* 3.9 13.5 - - - +
138A ASN* 3.0 26.9 + - - +
140A VAL* 1.3 79.2 - - - +
142A VAL* 1.3 58.5 + - - +
144A ASN* 3.4 9.5 + - - +
145A ARG* 3.0 27.5 + - - +
179A ILE* 4.1 17.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 3.7 22.4 - - + -
133A LEU* 4.0 8.5 - - + -
136A ILE* 3.7 28.5 - - + -
138A ASN 4.0 1.8 - - - +
139A PRO 3.0 10.0 + - - +
141A SER* 1.3 74.2 - - - +
143A ALA* 1.3 66.8 + - - +
145A ARG* 3.1 3.3 + - - +
146A LEU* 2.9 25.2 + - + +
165A LEU* 6.2 0.4 - - + -
170A ALA* 4.5 6.5 - - + +
173A TRP* 4.1 17.5 - - + -
174A ALA* 3.9 20.4 - - + -
179A ILE* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ALA 4.0 11.2 - - - +
118A SER* 4.1 4.3 - - - +
119A ILE* 3.6 11.1 - - + +
128A GLY* 3.4 37.1 - - - +
129A ALA* 3.9 13.0 - - - +
130A VAL* 4.3 2.8 - - - +
139A PRO 3.1 8.9 + - - +
140A VAL* 3.2 9.4 + - - +
142A VAL* 1.3 79.4 - - - +
144A ASN* 1.3 61.7 + - - +
146A LEU* 3.4 4.1 + - - -
147A LEU 3.1 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A THR* 4.1 12.0 + - - -
84A ASP* 3.5 19.7 + - - +
87A THR* 3.3 34.0 + - + +
119A ILE* 3.8 18.0 - - + +
140A VAL 2.8 17.2 + - - +
141A SER* 3.5 6.4 + - - +
143A ALA* 1.3 78.7 - - - +
145A ARG* 1.3 58.6 + - - +
147A LEU* 3.2 6.0 + - - +
148A CYS* 2.9 38.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A SER 3.0 17.2 + - - +
142A VAL 3.1 4.5 + - - +
144A ASN* 1.3 75.8 - - - +
146A LEU* 1.3 65.4 + - - +
148A CYS* 3.4 14.7 + - - +
149A GLU* 2.7 53.0 + - - +
152A LYS* 4.1 11.3 - - - +
173A TRP* 3.7 20.4 - - + -
177A HIS* 3.3 39.5 + - + +
179A ILE* 4.4 10.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
127A PHE 4.8 1.5 - - - +
128A GLY* 4.3 7.0 - - - -
129A ALA 3.4 27.8 - - - +
130A VAL* 4.0 17.0 - - + -
142A VAL* 2.9 13.9 + - + +
143A ALA 3.7 6.5 - - - +
144A ASN 3.3 0.2 - - - -
145A ARG* 1.3 76.4 - - - +
147A LEU* 1.3 58.4 + - - +
149A GLU* 3.5 2.5 + - + +
150A GLY* 2.9 24.9 + - - -
162A PRO* 3.8 29.0 - - + +
163A CYS* 3.9 8.7 - - - +
165A LEU* 3.8 25.8 - - + -
173A TRP* 3.4 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A THR* 4.3 13.5 - - + +
119A ILE* 3.8 43.3 - - + +
120A MSE 4.2 0.2 - - - -
121A ASP* 4.1 18.4 - - + +
126A ASN* 3.9 32.9 - - + +
127A PHE 4.0 16.6 - - - +
128A GLY* 4.2 0.4 - - - -
143A ALA 3.1 12.7 + - - +
144A ASN* 3.3 10.8 - - - +
146A LEU* 1.3 77.1 - - - +
148A CYS* 1.3 68.0 + - - +
150A GLY* 3.1 3.7 + - - -
151A GLN* 3.1 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 6.2 3.6 - - - -
83A THR* 5.6 3.1 - - - -
84A ASP* 5.1 6.1 - - - -
144A ASN* 2.9 36.4 + - - -
145A ARG* 3.7 22.2 - - - +
146A LEU 3.3 0.2 - - - -
147A LEU* 1.3 81.5 - - - +
149A GLU* 1.3 64.3 + - - +
151A GLN* 3.0 17.7 + - - +
152A LYS* 3.1 19.6 + - - +
----------------------------------------------------------
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 ARG* 2.7 57.4 + - - +
146A LEU* 3.8 4.3 - - - +
148A CYS* 1.3 76.1 - - - +
150A GLY* 1.3 62.8 + - - +
152A LYS* 2.9 41.8 + - - +
153A GLY* 3.0 9.9 + - - -
161A PRO* 4.0 14.0 - - + +
173A TRP* 3.9 24.7 - - + -
177A HIS* 4.5 8.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASN* 3.5 18.6 - - - +
146A LEU 2.9 15.0 + - - -
147A LEU* 3.1 4.9 + - - -
149A GLU* 1.3 76.6 - - - +
151A GLN* 1.3 61.5 + - - +
153A GLY* 3.2 10.4 + - - -
154A LYS* 3.6 12.6 + - - +
160A ILE* 5.8 2.4 - - - +
161A PRO* 4.1 22.7 - - - +
162A PRO 5.6 1.1 - - - -
299B ARG* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ASP* 5.0 0.6 + - - +
124A SER* 3.0 29.6 - - - +
126A ASN* 2.8 24.1 - - - +
147A LEU* 3.1 25.8 + - + +
148A CYS* 3.0 13.3 + - - +
150A GLY* 1.3 74.3 - - - +
152A LYS* 1.3 66.4 + - + +
154A LYS* 3.2 30.2 + - - +
155A LEU* 3.1 22.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ARG* 4.1 10.0 - - - +
148A CYS* 3.1 17.1 + - - +
149A GLU* 2.9 45.1 + - - +
151A GLN* 1.3 75.7 - - + +
153A GLY* 1.3 61.2 + - - +
154A LYS 3.4 0.7 + - - -
155A LEU* 3.5 20.3 + - - +
157A ALA* 3.7 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A GLU 3.0 11.7 + - - -
150A GLY 3.2 6.9 + - - -
151A GLN 3.1 0.8 - - - -
152A LYS* 1.3 76.9 - - - +
154A LYS* 1.3 61.4 + - - +
155A LEU 3.4 0.2 - - - -
156A SER* 4.2 0.3 - - - -
157A ALA* 3.3 35.7 + - - +
158A GLY 4.6 3.1 - - - +
160A ILE* 5.9 0.9 - - - -
161A PRO* 4.1 20.0 - - - +
----------------------------------------------------------
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