Contacts of the helix formed by residues 151 - 164 (chain A) in PDB entry 4IYM
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 GLY 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A LEU* 4.5 0.4 - - - +
99A ASP* 3.2 7.8 + - - -
100A ILE* 4.2 4.7 - - - -
149A PHE 3.1 0.4 - - - -
150A PRO* 1.3 81.5 - - - +
152A MSE 1.3 66.0 + - - +
153A ILE 3.5 0.2 - - - -
154A PRO* 3.4 4.0 - - - +
155A MSE 3.3 43.8 + - - +
179A VAL* 4.0 15.8 - - - +
183A LEU* 4.0 2.4 - - - +
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Residues in contact with MSE 152 (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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99A ASP* 2.7 33.1 + - - +
102A ARG* 3.3 55.6 - - + +
103A GLY* 3.8 9.3 - - - +
149A PHE* 3.5 40.8 + - + -
151A GLY* 1.3 72.3 - - - +
153A ILE* 1.3 68.0 + - + +
155A MSE 3.3 3.5 + - - +
156A TRP* 2.8 69.3 + - + +
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Residues in contact with ILE 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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145A THR* 3.6 19.5 - - + -
146A PRO* 3.7 18.2 - - + -
148A ASN* 4.2 4.7 - - - +
149A PHE* 3.2 26.0 + - + +
152A MSE 1.3 92.7 - - + +
154A PRO* 1.3 74.8 - - + +
156A TRP* 3.1 34.9 - - + +
157A MSE 3.3 14.6 + - + +
222A VAL* 3.6 41.1 - - + -
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Residues in contact with PRO 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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145A THR* 3.9 26.5 - - + +
149A PHE 3.3 15.3 - - - +
150A PRO* 3.3 20.9 - - + +
151A GLY 3.4 9.0 - - - +
153A ILE* 1.3 91.8 - - + +
155A MSE 1.3 57.2 + - - +
157A MSE 3.1 4.9 + - + +
158A PHE* 2.8 40.8 + - + +
168A PHE* 5.0 0.7 - - - -
170A LEU* 3.8 28.9 - - + -
180A PRO* 4.6 3.8 - - + -
183A LEU* 4.7 4.5 - - + -
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Residues in contact with MSE 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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70A PHE* 4.0 9.9 - - - -
74A LEU* 3.8 22.2 - - + -
100A ILE* 3.6 36.1 - - + +
103A GLY* 3.6 32.3 - - - +
106A VAL* 3.9 3.3 - - - +
107A CYS* 4.0 6.7 - - - -
151A GLY* 3.3 35.6 + - - +
152A MSE 3.3 1.6 + - - -
153A ILE 3.2 0.6 - - - -
154A PRO* 1.3 72.9 - - - +
156A TRP* 1.3 66.1 + - - +
158A PHE* 3.5 28.7 - - + -
159A ALA* 3.1 28.8 + - - +
160A PRO* 3.8 0.2 - - - +
183A LEU* 4.0 15.3 - - + -
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Residues in contact with TRP 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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102A ARG* 4.7 2.8 + - - +
106A VAL* 3.7 28.3 - - + +
152A MSE 2.8 65.4 + - + +
153A ILE* 3.1 32.8 - - + +
155A MSE 1.3 74.8 - - - +
157A MSE 1.3 57.8 + - - +
160A PRO* 3.0 24.4 - - - +
222A VAL* 4.2 10.3 - - + -
441A VAL* 5.1 6.3 - - + -
448A PHE* 3.5 55.0 - + - -
461A GLN* 3.6 32.9 - - + +
462A HIS* 3.8 27.6 + + + -
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Residues in contact with MSE 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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143A GLY* 3.6 26.9 - - - -
144A ILE 3.6 15.3 - - - +
145A THR* 3.8 16.2 - - - -
153A ILE* 3.5 15.9 - - + +
154A PRO* 3.1 4.6 + - - +
155A MSE 3.1 0.4 - - - -
156A TRP* 1.3 77.4 - - - +
158A PHE* 1.3 64.8 + - - +
159A ALA 3.4 0.2 - - - -
160A PRO* 3.5 5.2 - - - +
161A ALA* 3.3 24.3 + - - +
168A PHE* 3.6 15.3 - - + -
170A LEU* 5.2 0.4 - - - -
220A SER* 3.4 43.1 - - - +
222A VAL* 3.7 16.8 - - + +
243A GLN* 6.1 0.2 - - - -
461A GLN* 3.7 22.0 - - - +
470A TRP* 3.7 7.2 + - + +
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Residues in contact with PHE 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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67A PHE* 4.9 1.8 - + - -
70A PHE* 4.4 15.9 - + - -
107A CYS* 5.2 0.4 - - - -
154A PRO* 2.8 42.7 + - + -
155A MSE 3.5 28.3 - - + -
157A MSE 1.3 72.6 - - - +
159A ALA* 1.3 66.4 - - + +
161A ALA* 4.3 0.2 - - - -
162A ILE* 2.9 45.9 + - + +
168A PHE* 3.4 32.1 - + + -
170A LEU* 4.9 7.4 - - + -
183A LEU* 4.4 12.8 - - + -
187A MSE 4.3 19.1 - - + -
197A LEU* 3.9 32.5 - - + -
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Residues in contact with ALA 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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67A PHE* 3.4 24.7 - - + -
106A VAL* 3.8 13.5 - - + -
107A CYS* 4.1 15.9 - - - -
110A VAL* 3.8 12.3 - - + -
155A MSE 3.1 19.4 + - - +
158A PHE* 1.3 79.7 - - + +
160A PRO* 1.4 62.3 - - + +
163A ALA* 2.9 32.1 + - - +
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Residues in contact with PRO 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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106A VAL* 4.0 8.3 - - + -
110A VAL* 3.7 14.8 - - + -
156A TRP 3.0 28.7 - - - +
157A MSE 3.5 7.0 - - - +
159A ALA* 1.4 91.7 - - + +
161A ALA* 1.3 63.5 + - - +
163A ALA* 3.8 1.5 - - + +
164A CYS* 3.0 29.1 + - - -
462A HIS* 5.1 0.2 - - - -
466A SER* 3.3 35.4 - - - +
467A ILE* 4.3 9.4 - - + -
470A TRP* 3.9 11.2 - - + +
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Residues in contact with ALA 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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157A MSE 3.3 19.5 + - - +
158A PHE 3.9 0.7 - - - +
160A PRO* 1.3 79.8 - - - +
162A ILE* 1.3 62.5 + - - +
164A CYS 3.4 1.9 + - - -
166A ASN* 2.8 35.2 + - + +
168A PHE* 3.6 23.3 - - + -
470A TRP* 3.4 37.6 - - + -
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Residues in contact with ILE 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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55A TRP* 2.8 38.9 + - + +
67A PHE* 3.9 12.8 - - + -
158A PHE* 2.9 41.0 + - + +
161A ALA* 1.3 72.0 - - - +
163A ALA* 1.3 62.3 + - - +
165A GLY 2.9 10.0 + - - -
166A ASN 3.6 14.1 - - - +
168A PHE* 3.9 13.9 - - + -
187A MSE 4.2 2.5 - - + -
192A LEU* 3.6 31.4 - - + -
196A ILE* 3.8 10.8 - - + +
197A LEU* 3.7 30.1 - - + -
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Residues in contact with ALA 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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63A ARG* 3.0 30.1 + - - +
67A PHE* 3.7 17.1 - - + -
110A VAL* 3.6 25.8 - - + +
113A ILE* 3.4 28.5 - - + +
159A ALA 2.9 19.8 + - - +
160A PRO 3.8 3.8 - - - +
162A ILE* 1.3 76.2 - - - +
164A CYS* 1.3 56.0 + - - +
165A GLY 3.2 0.2 - - - -
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Residues in contact with CYS 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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63A ARG* 3.9 5.1 + - - -
113A ILE* 3.9 17.7 - - - -
117A GLN* 3.4 22.2 + - - -
137A PRO* 3.4 16.6 - - - +
160A PRO 3.0 23.3 + - - +
162A ILE 3.2 0.2 - - - -
163A ALA* 1.3 74.3 - - - +
165A GLY* 1.3 57.1 + - - +
166A ASN* 3.5 17.9 - - - +
467A ILE* 4.0 22.0 - - - -
470A TRP* 3.8 7.0 - - - +
471A THR* 3.6 28.5 - - + -
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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