Contacts of the helix formed by residues 140 - 156 (chain O) in PDB entry 3EXG
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 ALA 140 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135O ASN* 5.3 5.2 - - + -
137O ILE* 3.0 33.7 + - + +
139O GLY* 1.3 75.0 - - - +
141O GLN* 1.3 61.4 + - - +
142O VAL 3.0 1.4 + - - -
143O PRO* 3.3 4.9 - - - +
144O LEU* 3.4 12.4 - - + +
174O GLN* 3.3 15.8 - - - +
91P ASP* 3.9 14.4 - - - +
92P GLN* 3.3 19.8 + - - +
96P SER* 4.2 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86O ILE* 3.8 8.3 - - + +
87O THR* 3.4 23.1 - - - +
88O ALA* 3.1 30.6 - - - +
135O ASN* 3.7 15.5 - - + +
137O ILE 3.9 4.1 + - - +
139O GLY 2.9 25.9 + - - +
140O ALA* 1.3 74.7 + - - +
142O VAL* 1.3 64.9 + - + +
144O LEU* 3.7 13.1 - - - +
145O GLY* 2.9 22.2 + - - -
163O THR* 3.7 6.6 - - + +
164O LEU 3.4 25.4 + - - +
165O TYR* 3.4 14.5 - - - +
166O GLY 4.9 0.4 - - - +
169O ALA* 5.3 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139O GLY 2.9 12.4 + - - +
141O GLN* 1.3 83.5 - - + +
143O PRO* 1.3 72.4 - - + +
145O GLY* 3.1 9.2 + - - -
146O ALA* 3.2 13.7 + - - +
163O THR* 3.6 8.5 - - + +
165O TYR* 3.8 29.8 - - + -
175O ILE* 3.4 37.7 - - + -
178O ALA* 4.1 10.1 - - + +
191O PHE* 3.7 30.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 143 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139O GLY 3.1 14.6 - - - +
140O ALA 3.3 4.9 - - - +
142O VAL* 1.3 93.4 - - + +
144O LEU* 1.3 62.3 + - - +
146O ALA 3.3 1.9 + - - -
147O GLY 3.0 16.6 + - - -
174O GLN* 3.4 40.4 - - + +
178O ALA* 4.4 8.3 - - + -
60P MET 4.4 0.2 - - - +
61P GLY* 3.6 17.3 - - - +
64P GLY* 3.5 26.7 - - - -
65P ILE* 3.5 14.4 - - + +
92P GLN* 3.8 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86O ILE* 3.6 19.7 - - + -
135O ASN* 3.7 22.9 - - + +
140O ALA* 3.4 17.9 + - + +
141O GLN* 3.7 4.7 - - - +
142O VAL 3.3 0.4 - - - -
143O PRO* 1.3 76.1 - - - +
145O GLY* 1.3 57.0 + - - +
147O GLY* 2.9 2.4 + - - -
148O ILE* 2.8 32.5 + - + +
64P GLY 3.4 20.2 - - - +
67P VAL* 3.5 20.4 - - + -
68P GLY* 3.5 21.3 - - - +
71P MET* 4.4 11.4 - - + -
92P GLN* 3.7 11.0 - - - +
96P SER* 4.0 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86O ILE* 4.0 10.3 - - - +
141O GLN 2.9 16.2 + - - -
142O VAL 3.1 3.5 + - - -
144O LEU* 1.3 76.1 - - - +
146O ALA* 1.3 57.5 + - - +
147O GLY 3.0 0.2 + - - -
148O ILE* 3.2 2.3 + - - -
149O ALA* 2.9 26.9 + - - +
161O CYS* 3.5 10.4 - - - -
163O THR* 3.2 24.7 - - - -
189O CYS* 4.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142O VAL 3.2 12.2 + - - +
143O PRO 3.9 5.6 - - - +
145O GLY* 1.3 74.1 - - - +
147O GLY* 1.3 53.6 + - - +
149O ALA* 3.6 3.8 - - - -
150O LEU* 2.8 32.2 + - - +
178O ALA* 4.6 7.6 - - + +
182O ALA* 4.6 3.4 - - + -
187O LEU* 3.6 20.4 - - + +
189O CYS* 4.0 19.4 - - - -
191O PHE* 4.4 11.2 - - + -
65P ILE* 4.1 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 147 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143O PRO 3.0 6.9 + - - -
144O LEU 2.9 9.1 + - - -
146O ALA* 1.3 75.8 - - - +
148O ILE* 1.3 64.5 + - - +
150O LEU* 3.2 12.1 + - - +
151O ALA* 3.2 9.2 + - - +
65P ILE* 3.4 34.3 - - - +
68P GLY 3.8 7.0 - - - -
69P ALA* 3.6 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 148 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84O HIS* 3.4 40.2 - - + +
86O ILE* 3.9 20.9 - - + -
132O TYR* 3.3 48.7 - - + +
144O LEU* 2.8 16.6 + - + +
145O GLY* 3.6 6.3 - - - +
147O GLY* 1.3 76.5 - - - +
149O ALA* 1.3 60.7 + - - +
151O ALA* 3.1 5.5 + - - +
152O CYS* 3.1 21.3 + - - -
161O CYS* 3.8 9.9 - - + -
68P GLY* 3.4 20.9 - - - +
71P MET* 5.2 1.1 - - + -
72P ALA* 4.2 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145O GLY 2.9 13.0 + - - +
146O ALA 3.6 4.7 - - - +
147O GLY 3.2 0.2 - - - -
148O ILE* 1.3 75.6 - - - +
150O LEU* 1.3 65.5 + - - +
151O ALA 3.2 0.2 + - - -
152O CYS* 3.3 5.1 + - - +
153O LYS 3.2 17.0 + - - -
161O CYS* 3.8 9.6 - - + +
187O LEU* 4.4 4.5 - - + -
188O PRO* 3.4 28.7 - - - +
189O CYS* 3.4 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146O ALA 2.8 18.3 + - - +
147O GLY* 3.3 8.7 - - - +
149O ALA* 1.3 74.5 - - - +
151O ALA* 1.3 58.9 + - - +
153O LYS* 3.4 9.5 + - + +
154O TYR* 3.0 35.2 + - + +
185O TRP* 4.7 12.3 - - + -
187O LEU* 3.6 29.8 - - + +
24P PHE* 3.9 34.5 - - + -
26P LEU* 5.9 0.9 - - + -
53P ILE* 4.7 15.3 - - + -
65P ILE* 4.1 18.8 - - + -
69P ALA* 4.4 7.0 - - + -
74P LEU* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147O GLY 3.2 6.0 + - - +
148O ILE 3.3 9.4 - - - +
149O ALA 3.1 0.6 - - - -
150O LEU* 1.3 78.3 - - - +
152O CYS* 1.3 68.8 + - - +
154O TYR* 3.1 1.5 + - - +
155O ASN* 2.9 31.3 + - - +
69P ALA* 4.5 1.1 - - + +
72P ALA* 3.7 23.8 - - + -
74P LEU* 3.2 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 152 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84O HIS* 3.9 20.0 - - - -
148O ILE* 3.1 15.9 + - - -
149O ALA* 3.4 10.8 - - - +
151O ALA* 1.3 78.0 - - - +
153O LYS* 1.3 64.7 + - - +
154O TYR 2.8 1.9 + - - -
155O ASN* 2.9 9.8 + - - +
156O GLY* 3.3 9.5 + - - -
157O LYS 4.2 4.1 + - - -
158O ASP 5.3 1.1 + - - -
159O GLU* 3.2 56.0 - - + +
160O VAL 4.1 8.5 - - - -
188O PRO* 3.8 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149O ALA 3.2 2.8 + - - +
150O LEU* 3.5 14.3 - - + +
152O CYS* 1.3 78.1 - - - +
154O TYR* 1.3 61.9 + - - +
156O GLY* 3.6 10.9 + - - +
185O TRP* 2.9 39.6 + - - +
186O LYS* 3.9 12.8 - - - +
187O LEU* 4.1 10.1 - - + -
188O PRO* 3.7 22.0 - - + +
50P LYS* 5.5 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 154 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150O LEU* 3.0 25.5 + - + +
151O ALA* 3.5 6.1 - - - +
152O CYS 2.8 2.8 + - - -
153O LYS* 1.3 80.5 - - + +
155O ASN* 1.3 64.0 + - - +
156O GLY 3.7 0.2 + - - -
21P GLU* 2.6 29.8 + - + -
22P LYS* 4.1 3.5 - - - -
23P VAL 4.1 0.7 + - - -
24P PHE* 4.1 19.3 - + + +
50P LYS* 3.1 76.6 + - + +
51P ARG* 3.0 20.2 + - - -
53P ILE* 6.0 1.8 - - + -
74P LEU* 3.8 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 155 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151O ALA* 2.9 25.9 + - - +
152O CYS* 2.9 6.5 + - - +
154O TYR* 1.3 82.5 - - - +
156O GLY* 1.3 67.1 + - - +
157O LYS* 3.7 22.3 - - + +
159O GLU* 4.8 6.7 + - - +
22P LYS* 5.2 6.8 - - - +
72P ALA 5.3 3.6 + - - -
74P LEU* 4.1 26.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 156 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152O CYS 3.3 5.5 + - - -
153O LYS 3.6 9.3 + - - -
154O TYR 3.3 3.2 - - - -
155O ASN* 1.3 81.0 - - - +
157O LYS* 1.3 67.3 + - - +
158O ASP* 3.6 2.2 - - - -
----------------------------------------------------------
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