Contacts of the helix formed by residues 139 - 154 (chain B) in PDB entry 3SFX
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 HIS 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A TYR* 3.5 50.1 - + + +
110A GLN* 5.9 0.8 + - - -
128B PHE 2.9 9.6 + - - +
138B PRO* 1.3 76.9 - - - +
140B LEU* 1.3 65.0 + - - +
141B LEU* 3.1 32.2 + - + -
142B PRO* 3.3 12.8 - - + +
143B THR* 2.9 22.5 + - - -
175B PHE* 3.6 4.2 - - - -
188B VAL* 3.2 37.7 - - + +
189B CYS* 3.8 12.8 - - + -
193B GLU* 4.6 3.6 + - - -
197B ARG* 5.1 1.1 - - - -
527B SO4 3.2 27.0 + - - -
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B HIS* 1.3 71.8 + - - +
141B LEU* 1.3 60.6 + - + +
143B THR* 3.3 5.8 + - - +
144B TYR 3.1 22.2 + - - -
175B PHE* 3.8 10.5 - - + -
176B PHE* 3.6 37.6 - - + -
179B CYS* 4.2 6.1 - - + -
186B PHE* 3.9 14.6 - - + -
187B VAL 3.4 20.9 - - - +
188B VAL* 2.8 21.0 + - - +
198B GLY* 3.5 42.0 - - - +
201B CYS* 3.4 12.3 - - + +
202B LEU* 4.0 11.9 - - + +
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TRP* 3.8 11.4 - - + +
139B HIS* 3.1 13.6 + - + +
140B LEU* 1.3 75.5 - - - +
142B PRO* 1.4 64.0 - - + +
144B TYR* 3.1 6.9 + - - +
145B ALA* 3.0 25.1 + - - +
188B VAL* 4.1 7.4 - - + -
197B ARG* 3.5 31.9 - - + +
198B GLY* 3.9 25.4 - - - +
201B CYS* 3.9 18.8 - - - -
525B FII 3.6 27.1 - - + -
526B JAN 5.1 2.2 - - + -
527B SO4 3.3 34.3 - - - +
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Residues in contact with PRO 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A TYR* 4.3 0.4 - - - +
86B ALA 5.5 0.2 - - - +
87B SER* 6.2 0.2 - - - -
89B PRO* 3.6 20.8 - - + +
90B TRP* 4.7 2.0 - - + +
128B PHE* 3.7 2.9 - - - +
129B GLY 3.4 34.1 - - - +
130B GLY* 3.7 5.6 - - - +
139B HIS* 3.3 36.1 - - + +
141B LEU* 1.4 89.0 - - - +
143B THR* 1.3 54.1 + - - -
145B ALA* 3.7 3.4 - - + -
146B SER* 2.7 36.1 + - - -
527B SO4 3.3 18.1 - - - +
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Residues in contact with THR 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLY* 3.8 6.2 - - - -
128B PHE* 3.0 36.8 + - + +
139B HIS 2.9 23.1 + - - -
140B LEU* 3.5 9.2 - - - -
141B LEU 3.1 1.4 - - - -
142B PRO* 1.3 74.1 - - - +
144B TYR* 1.3 65.2 + - - +
146B SER* 4.0 0.5 - - - -
147B VAL* 3.0 33.1 + - + +
172B ILE* 4.8 6.7 - - + -
175B PHE* 4.1 2.9 - - - -
176B PHE* 4.2 21.3 - - + -
201B CYS 6.5 0.2 - - - -
205B VAL* 4.1 19.1 - - + -
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Residues in contact with TYR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B TRP* 3.5 34.1 - + - -
93B PHE* 4.0 15.6 - + - -
140B LEU 3.1 7.3 + - - -
141B LEU 3.1 4.0 + - - +
143B THR* 1.3 75.4 - - - +
145B ALA* 1.3 61.6 + - - +
147B VAL* 3.8 0.7 - - - +
148B CYS* 2.9 55.4 + - - -
200B TYR* 3.4 31.4 + + - -
201B CYS* 3.5 30.5 - - + +
204B VAL* 3.7 30.7 - - + -
205B VAL* 3.8 10.4 - - + +
501B PHE 2.8 20.9 + - - -
502B ASN* 3.9 9.5 + - - +
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PRO* 3.5 33.4 - - + +
90B TRP* 3.8 26.9 - - + +
93B PHE* 3.9 8.5 - - + +
141B LEU 3.0 15.3 + - - +
142B PRO* 4.0 0.9 - - + +
144B TYR* 1.3 83.7 - - - +
146B SER* 1.3 54.2 + - - +
148B CYS* 3.6 0.9 + - - -
149B SER* 2.8 37.6 + - - -
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Residues in contact with SER 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PRO* 3.6 15.3 - - - +
118B LEU* 3.9 18.3 - - - +
121B PHE* 4.7 0.7 - - - -
128B PHE* 3.4 42.9 - - - +
142B PRO 2.7 23.4 + - - -
145B ALA* 1.3 74.3 - - - +
147B VAL* 1.3 61.0 + - - +
149B SER* 3.3 1.7 + - - -
150B LEU* 2.9 36.1 + - - +
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 4.1 18.2 - - + -
143B THR* 3.0 23.7 + - + +
144B TYR 3.9 2.5 - - - +
146B SER* 1.3 77.0 - - - +
148B CYS* 1.3 63.4 + - - +
150B LEU* 3.2 7.9 + - - +
151B ALA* 3.0 18.2 + - - +
165B LEU* 4.1 15.9 - - + -
172B ILE* 5.5 0.2 - - + -
205B VAL* 4.0 28.5 - - + -
208B LEU* 4.1 16.2 - - + -
209B LEU* 4.6 8.7 - - + -
511B PHE* 3.7 29.1 - - + -
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Residues in contact with CYS 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PHE* 3.6 24.5 - - + -
144B TYR* 2.9 54.3 + - - +
145B ALA 4.0 0.2 - - - +
147B VAL* 1.3 77.0 - - - +
149B SER* 1.3 57.9 + - - +
151B ALA* 3.1 11.6 + - - +
152B ILE* 3.0 30.2 + - - +
204B VAL* 4.6 8.5 - - - -
208B LEU* 4.8 8.7 - - - -
501B PHE* 4.4 3.4 - - - -
503B ILE* 3.9 16.3 - - + +
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PRO 4.1 0.7 + - - -
92B VAL* 3.5 11.9 - - - +
93B PHE* 3.2 29.5 + - - -
96B VAL* 4.1 13.2 - - - +
114B VAL* 4.9 0.4 - - - -
118B LEU* 3.5 24.5 - - - -
145B ALA 2.8 23.0 + - - -
146B SER* 3.3 0.6 + - - -
148B CYS* 1.3 73.2 - - - +
150B LEU* 1.3 60.8 + - - +
152B ILE* 3.2 2.7 + - - +
153B ALA* 2.8 33.8 + - - +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B VAL* 4.0 37.9 - - + +
118B LEU* 4.0 18.8 - - + -
119B LEU* 4.6 10.1 - - + -
128B PHE* 3.9 21.8 - - + -
146B SER 2.9 20.7 + - - +
147B VAL 3.6 5.2 - - - +
149B SER* 1.3 75.3 - - - +
151B ALA* 1.3 57.6 + - - +
154B GLY* 2.8 18.8 + - - +
160B GLY 4.8 0.7 - - - +
161B GLY* 4.5 9.9 - - - +
162B TRP* 2.8 24.7 + - + -
165B LEU* 3.8 35.0 - - + -
511B PHE* 4.0 1.8 - - + -
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B VAL 3.0 10.6 + - - +
148B CYS* 3.1 11.6 + - - +
150B LEU* 1.3 77.1 - - - +
152B ILE* 1.3 61.1 + - - +
154B GLY 4.6 1.0 + - - +
162B TRP* 4.1 11.8 - - - -
208B LEU* 5.9 0.2 - - + -
503B ILE* 3.8 23.3 - - + -
507B ARG* 3.7 18.1 - - - +
511B PHE* 3.4 42.1 - - + -
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Residues in contact with ILE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B PHE* 4.1 7.4 - - + -
96B VAL* 3.7 35.9 - - + +
97B HIS* 3.7 34.5 - - + +
100B ASP* 3.4 26.2 - - - +
106B LEU* 6.2 1.1 - - + -
111B LYS* 4.7 4.3 + - - -
148B CYS 3.0 19.1 + - - +
149B SER 3.2 6.0 + - - +
151B ALA* 1.3 79.9 - - - +
153B ALA* 1.3 59.8 + - + +
154B GLY 3.7 1.6 - - - +
503B ILE* 4.0 20.0 - - + -
507B ARG* 3.4 34.6 + - + +
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B VAL* 5.0 4.9 - - + -
106B LEU* 5.1 3.1 - - + -
108B GLN* 4.9 1.9 - - - +
111B LYS* 3.4 43.3 - - + +
114B VAL* 3.7 32.5 - - + -
115B VAL* 3.9 8.4 - - + +
149B SER 2.8 18.1 + - - +
150B LEU* 5.3 0.2 - - - -
152B ILE* 1.3 76.0 - - + +
154B GLY* 1.3 63.1 + - - +
155B ASN* 4.9 1.4 + - - -
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Residues in contact with GLY 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LYS* 5.6 2.8 + - - -
115B VAL* 3.8 9.6 - - - +
150B LEU 2.8 17.8 + - - -
151B ALA 4.7 2.1 - - - +
152B ILE 3.7 2.0 - - - +
153B ALA* 1.3 82.1 - - - +
155B ASN* 1.3 65.8 + - - +
160B GLY 3.2 15.0 - - - -
162B TRP* 3.4 14.3 - - - -
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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
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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) + - + + + + + -
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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