Contacts of the helix formed by residues 152 - 166 (chain A) in PDB entry 2FBW
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 ARG 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ALA 3.8 5.6 - - - -
149A VAL 2.9 12.0 + - - +
150A ALA* 4.7 0.4 - - - +
151A ASP* 1.3 86.7 - - - +
153A THR* 1.3 63.7 + - - +
154A GLY 3.3 3.1 + - - -
155A HIS* 3.4 21.3 + - + -
156A SER* 3.2 21.7 + - - -
338A PRO* 3.7 28.2 + - - +
339A GLY* 3.9 24.9 - - - +
342A GLU* 6.2 1.0 - - - +
69B ILE* 5.6 7.4 - - + -
156B TYR* 2.9 35.5 + - + +
157B GLU* 3.6 30.8 + - - +
227B LYS* 6.0 4.8 - - - +
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Residues in contact with THR 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ALA 3.5 0.4 + - - -
61A GLN 3.0 21.7 + - - -
63A GLY* 3.4 25.7 - - - -
64A ILE* 4.3 3.4 - - + -
115A MET* 3.4 23.5 - - + +
147A CYS 4.0 8.1 - - - +
148A CYS* 3.3 8.7 - - - +
149A VAL* 3.0 27.6 + - - +
150A ALA 4.1 0.3 + - - -
152A ARG* 1.3 76.2 - - - +
154A GLY* 1.3 59.4 + - - +
156A SER* 3.3 1.4 + - - -
157A LEU* 2.8 26.5 + - - +
414A LEU* 4.0 11.0 - - + -
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Residues in contact with GLY 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A THR* 3.2 24.5 - - - +
58A VAL 3.9 0.2 - - - -
60A ALA* 2.7 30.0 + - - +
153A THR* 1.3 70.5 - - - +
155A HIS* 1.3 57.3 + - - -
157A LEU* 3.6 7.2 - - - +
158A LEU* 2.8 34.5 + - - +
414A LEU* 4.3 4.4 - - - +
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Residues in contact with HIS 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A VAL* 3.2 30.6 + - - +
60A ALA 3.8 1.6 + - - +
152A ARG* 3.4 22.6 + - + +
154A GLY* 1.3 75.6 - - - +
156A SER* 1.3 69.4 + - - +
158A LEU* 4.0 0.2 - - - -
159A HIS* 3.0 61.8 + + - +
69B ILE* 3.9 18.7 - - + +
156B TYR* 2.9 32.6 + + - -
157B GLU* 3.6 13.3 + - - -
158B CYS 3.0 27.5 + - - -
159B ILE* 4.2 5.5 - - + +
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Residues in contact with SER 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A MET* 4.1 2.2 - - - -
116A PRO* 3.6 16.2 - - - +
149A VAL* 3.5 32.9 - - - +
152A ARG 3.2 7.1 + - - -
153A THR 3.9 0.4 - - - -
155A HIS* 1.3 79.9 - - - +
157A LEU* 1.3 63.6 + - - +
159A HIS* 4.3 3.0 - - - +
160A THR* 2.5 33.9 + - - -
156B TYR* 3.4 28.8 - - - -
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLY* 4.3 6.1 - - - -
57A THR* 3.7 22.0 - - + -
64A ILE* 4.4 5.8 - - + -
110A LEU* 3.7 32.9 - - + +
115A MET* 3.8 19.2 - - + +
153A THR 2.8 21.6 + - - +
154A GLY* 3.2 6.0 + - - +
156A SER* 1.3 72.8 - - - +
158A LEU* 1.3 59.3 + - - +
160A THR* 3.6 1.7 - - - -
161A LEU* 3.0 51.3 + - + +
414A LEU* 4.0 35.0 - - + +
417A LEU* 5.0 1.3 - - + -
418A VAL* 4.7 4.9 - - + -
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA 3.9 4.3 - - - +
27A GLY* 3.7 23.6 - - - -
28A GLY* 3.9 4.9 - - - +
31A LEU* 3.7 27.6 - - + -
52A PRO 3.4 21.1 - - - +
53A THR* 3.5 14.8 - - + -
55A SER* 3.9 7.6 - - - +
57A THR* 3.9 7.6 - - + -
58A VAL* 3.5 34.3 - - + +
154A GLY 2.8 20.7 + - - +
155A HIS 4.1 1.8 - - - +
157A LEU* 1.3 76.4 - - - +
159A HIS* 1.3 58.7 + - - +
161A LEU* 3.4 2.5 + - + -
162A TYR* 2.9 30.3 + - - +
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Residues in contact with HIS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A THR* 3.6 35.5 + - + +
58A VAL* 4.0 12.6 - - + +
155A HIS* 3.0 57.6 + + - +
156A SER* 4.3 3.6 - - - +
158A LEU* 1.3 76.3 - - - +
160A THR* 1.3 58.2 + - - +
162A TYR* 3.4 6.1 + - - +
163A GLY* 3.0 26.2 + - - -
70B CYS 5.9 0.4 + - - -
122B TYR* 4.9 12.2 + - - +
127B PRO 5.3 0.9 - - - +
158B CYS 4.1 9.8 + - - -
159B ILE* 4.4 9.0 + - - -
160B LEU* 4.0 23.8 - - + +
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Residues in contact with THR 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 4.1 2.9 - - + +
113A TYR* 3.4 38.5 - - + +
114A GLY 4.3 1.6 - - - -
115A MET* 3.4 37.5 - - + +
116A PRO* 4.2 4.2 - - - +
156A SER 2.5 24.7 + - - -
157A LEU* 3.6 4.0 - - - -
159A HIS* 1.3 74.1 - - - +
161A LEU* 1.3 61.4 + - - +
163A GLY* 3.4 2.1 + - - -
164A ARG* 3.0 27.2 + - - +
128B TYR* 5.7 0.5 - - - +
189B ARG* 5.8 0.2 + - - -
190B TRP* 5.8 7.8 - - + -
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLY* 3.6 29.2 - - - +
31A LEU* 4.2 14.3 - - + +
32A ARG* 4.2 12.8 - - + +
35A PHE* 3.7 31.1 - - + -
110A LEU* 3.9 22.4 - - + -
113A TYR* 3.9 10.3 - - + -
157A LEU* 3.0 38.9 + - + +
158A LEU* 3.9 3.8 - - - +
160A THR* 1.3 76.0 - - - +
162A TYR* 1.3 57.6 + - - +
164A ARG* 3.4 4.0 + - - +
165A SER* 2.9 29.1 + - - -
418A VAL* 4.2 9.2 - - + -
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Residues in contact with TYR 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.9 12.7 - - + +
51A PHE* 3.4 32.2 - + - -
52A PRO* 3.8 32.1 - - + -
53A THR* 3.7 22.9 - - + -
158A LEU 2.9 18.9 + - - +
159A HIS* 3.8 4.0 - - - +
160A THR 3.2 0.2 - - - -
161A LEU* 1.3 76.6 - - - +
163A GLY* 1.3 64.1 + - - +
165A SER* 2.5 30.1 + - - -
166A LEU* 3.3 32.1 + - + +
172A TYR* 5.8 6.3 - + - -
119B TYR* 5.0 6.4 + - - +
122B TYR* 4.1 30.9 - + - -
123B LYS* 6.0 0.5 - - - +
160B LEU* 5.4 0.2 - - + -
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Residues in contact with GLY 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A HIS 3.0 15.1 + - - -
160A THR* 3.9 1.3 - - - -
162A TYR* 1.3 77.5 - - - +
164A ARG* 1.3 63.3 + - - +
166A LEU* 3.1 31.5 + - - +
122B TYR* 5.4 1.6 - - - -
127B PRO* 3.7 20.4 - - - -
128B TYR* 3.3 18.0 - - - -
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Residues in contact with ARG 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.8 24.2 - - + -
39A GLU* 5.3 0.8 + - - -
112A ASN 5.1 2.8 + - - -
113A TYR* 3.4 45.1 + - + +
160A THR 3.0 17.8 + - - +
161A LEU* 3.6 8.3 - - - +
162A TYR 3.3 0.2 - - - -
163A GLY* 1.3 75.0 - - - +
165A SER* 1.3 63.4 + - - +
167A ARG* 2.9 54.7 + - - +
168A TYR* 3.2 31.7 + - + -
128B TYR* 4.4 7.6 - - + +
129B LEU 5.2 1.6 + - - -
134B GLU* 4.4 6.8 + - - -
137B GLN* 3.3 34.6 + - - +
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Residues in contact with SER 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 4.4 4.9 - - - -
35A PHE* 4.1 23.7 - - - -
161A LEU 2.9 14.0 + - - -
162A TYR* 2.5 34.9 + - - -
164A ARG* 1.3 74.7 - - - +
166A LEU* 1.3 61.9 + - - +
167A ARG 3.1 1.7 + - - -
168A TYR* 3.3 19.8 + - - +
170A THR* 4.8 1.2 + - - -
172A TYR* 3.2 36.5 + - - -
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A TYR* 3.3 46.2 - - + +
163A GLY* 3.2 15.5 - - - +
164A ARG 3.0 0.8 - - - -
165A SER* 1.3 77.8 + - - +
167A ARG* 1.3 58.6 + - - +
168A TYR 3.4 4.2 + - - +
172A TYR* 6.1 2.9 - - + -
122B TYR* 4.7 1.8 - - + -
123B LYS* 4.2 51.8 + - + +
127B PRO* 3.8 34.1 - - + -
128B TYR* 4.4 10.8 + - + -
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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
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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