Contacts of the helix formed by residues 150 - 167 (chain A) in PDB entry 1TF4
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 SER 150 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A GLY* 1.3 73.5 - - - +
151A ASP* 1.3 58.5 + - - +
154A ALA* 3.0 34.0 + - - +
189A ALA* 2.9 35.7 + - - +
192A TYR 3.1 13.6 + - - -
193A ARG* 3.2 4.7 - - - +
194A GLY 2.9 18.1 + - - -
212A TYR* 3.7 28.0 - - - -
215A GLU* 4.4 0.2 - - - +
216A LEU* 5.0 3.8 - - - +
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Residues in contact with ASP 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 4.0 9.4 - - + -
149A GLY 3.7 1.4 - - - -
150A SER* 1.3 72.7 - - - +
152A VAL* 1.3 65.0 + - - +
155A GLU* 3.0 29.6 + - - +
195A VAL* 3.6 10.1 - - - +
196A TYR* 3.1 39.8 + - - +
208A SER* 2.6 35.0 + - - +
211A GLY 4.3 0.7 - - - +
212A TYR* 3.6 11.2 - - + +
215A GLU* 3.4 32.3 - - - +
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Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLY* 4.0 5.6 - - - +
64A PHE* 3.8 41.5 - - + +
67A ALA* 5.6 0.2 - - + -
114A LEU* 4.4 0.4 - - + -
116A VAL* 3.6 35.0 - - + -
143A VAL* 4.4 4.0 - - + -
149A GLY* 3.5 11.2 - - - +
151A ASP* 1.3 82.3 + - - +
153A ALA* 1.3 60.4 + - - +
155A GLU* 3.7 1.1 - - + +
156A THR* 2.8 38.8 + - - +
196A TYR* 3.5 31.0 - - + -
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Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU* 3.8 15.7 - - + -
149A GLY 3.0 20.2 + - - +
152A VAL* 1.3 75.0 - - + +
154A ALA* 1.3 61.6 + - - +
156A THR* 3.3 3.1 + - - -
157A ALA* 2.9 28.1 + - - +
185A LEU* 3.9 11.8 - - + +
188A PHE* 3.7 31.4 - - + -
189A ALA* 3.8 12.6 - - + -
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Residues in contact with ALA 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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150A SER 3.0 21.5 + - - +
153A ALA* 1.3 76.2 - - - +
155A GLU* 1.3 58.1 + - - +
157A ALA* 3.3 8.4 + - - +
158A ALA* 2.9 27.4 + - - +
186A TYR* 4.5 12.1 - - + -
189A ALA* 3.7 12.5 - - + +
215A GLU* 3.4 32.1 - - + +
216A LEU* 4.5 3.4 - - + +
219A GLY* 4.0 5.7 - - - -
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 4.1 15.0 - - + +
67A ALA* 3.6 6.3 - - + -
68A PHE* 3.5 31.3 - - - +
71A THR* 2.8 27.5 + - - -
151A ASP 3.0 17.9 + - - +
152A VAL 3.7 4.3 - - - +
153A ALA 3.2 0.2 - - - -
154A ALA* 1.3 76.2 - - - +
156A THR* 1.3 60.3 + - - +
158A ALA* 3.1 5.8 + - - +
159A ALA* 2.8 26.0 + - - +
215A GLU* 4.2 3.5 - - + +
218A TRP* 3.0 24.8 + - - -
263A LYS* 2.8 36.0 + - - +
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Residues in contact with THR 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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63A GLY 4.7 1.2 + - - -
67A ALA* 3.8 17.8 - - - +
104A PHE* 3.9 37.9 - - + -
114A LEU* 3.7 19.6 - - + +
152A VAL* 2.8 25.9 + - - +
153A ALA 3.7 4.5 - - - -
155A GLU* 1.3 75.3 - - - +
157A ALA* 1.3 61.7 + - - +
159A ALA* 3.3 2.7 + - - +
160A MET* 3.0 30.2 + - - +
185A LEU* 3.7 20.2 - - + -
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Residues in contact with ALA 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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153A ALA 2.9 17.2 + - - +
154A ALA* 3.4 7.4 - - - +
155A GLU 3.2 0.2 - - - -
156A THR* 1.3 77.4 - - - +
158A ALA* 1.3 56.6 + - - +
160A MET 3.3 0.9 + - - -
161A ALA* 2.8 31.6 + - - +
182A ALA* 3.3 39.5 - - + +
185A LEU* 3.9 5.3 - - + +
186A TYR* 3.9 20.4 - - + +
219A GLY* 5.6 0.4 - - - -
223A LEU* 4.9 3.4 - - + -
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Residues in contact with ALA 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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71A THR* 3.8 2.9 - - - +
154A ALA 2.9 14.2 + - - +
155A GLU 3.1 8.3 + - - +
157A ALA* 1.3 76.2 - - - +
159A ALA* 1.3 57.1 + - - +
161A ALA* 3.7 0.8 - - - +
162A ALA* 2.8 33.8 + - - +
218A TRP* 3.8 30.1 - - + +
219A GLY* 4.0 9.8 - - - -
222A TRP* 3.9 23.6 - - + +
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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 ALA 3.5 14.8 - - - +
70A ALA* 3.8 14.7 - - + +
71A THR* 3.2 23.7 + - - +
74A ALA* 5.1 0.9 - - - +
101A ASN* 4.3 0.9 - - - -
104A PHE* 4.0 13.9 - - + -
155A GLU 2.8 10.4 + - - +
156A THR* 3.5 9.6 - - - +
157A ALA 3.3 0.2 - - - -
158A ALA* 1.3 76.3 - - - +
160A MET* 1.3 54.9 + - - +
162A ALA* 4.0 1.0 - - - +
163A SER* 2.7 37.2 + - - -
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Residues in contact with MET 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASN* 3.7 17.0 - - - +
104A PHE* 3.9 27.8 - - + +
105A ILE* 3.7 31.4 - - + +
156A THR 3.0 13.1 + - - +
157A ALA 3.8 2.7 - - - +
159A ALA* 1.3 73.9 - - - +
161A ALA* 1.3 65.7 + - - +
163A SER* 3.5 0.7 + - - -
164A SER* 3.0 23.4 + - - -
178A LEU* 3.6 35.7 - - + +
181A HIS* 3.7 30.7 - - + +
182A ALA* 4.1 4.5 - - + -
185A LEU* 4.0 21.3 - - - -
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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 ALA 2.8 17.5 + - - +
158A ALA* 3.7 2.9 - - - +
160A MET* 1.3 76.9 - - - +
162A ALA* 1.3 61.7 + - - +
164A SER* 2.5 26.8 + - - -
165A ILE* 3.6 2.6 + - - +
179A VAL* 5.2 2.0 - - - -
182A ALA* 3.9 12.3 - - + +
222A TRP* 3.7 29.2 - - + +
223A LEU* 4.1 10.1 - - + +
226A ALA* 3.4 16.0 - - + +
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Residues in contact with ALA 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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71A THR* 4.3 12.3 - - + +
74A ALA* 3.8 18.4 - - + -
78A ILE* 3.6 9.1 - - + +
158A ALA 2.8 21.6 + - - +
159A ALA 4.0 1.8 - - - +
161A ALA* 1.3 74.8 - - - +
163A SER* 1.3 61.5 + - - +
165A ILE* 3.4 20.7 + - - +
166A VAL* 3.7 5.2 + - - +
222A TRP* 3.8 33.6 - - + +
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Residues in contact with SER 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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70A ALA* 4.8 2.6 + - - +
74A ALA* 4.2 9.0 - - - +
97A LEU* 4.1 14.5 - - - +
101A ASN* 3.1 33.5 + - - -
159A ALA 2.7 22.1 + - - -
160A MET 3.9 2.7 - - - -
161A ALA 3.3 0.2 - - - -
162A ALA* 1.3 74.0 - - - +
164A SER* 1.3 65.9 + - - +
166A VAL* 3.0 15.2 + - - +
167A PHE* 3.1 26.5 + - - -
178A LEU* 4.0 5.4 - - - -
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Residues in contact with SER 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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160A MET 3.0 14.7 + - - -
161A ALA 2.5 20.8 + - - -
163A SER* 1.3 76.6 - - - +
165A ILE* 1.3 53.5 + - - +
167A PHE 3.2 0.6 + - - +
168A ALA* 2.7 35.5 + - - +
175A ALA* 3.5 32.6 - - - +
178A LEU* 3.9 10.7 - - - +
179A VAL* 3.4 20.7 - - - +
226A ALA* 3.4 7.8 + - - +
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Residues in contact with ILE 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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78A ILE* 4.0 35.0 - - + -
161A ALA 3.7 14.4 - - - +
162A ALA* 3.5 10.5 - - - +
164A SER* 1.3 77.2 - - - +
166A VAL* 1.3 62.1 + - - +
168A ALA* 3.5 19.1 - - + +
169A ASP* 4.9 1.9 + - - +
222A TRP* 4.4 4.5 - - + -
225A LYS* 3.7 37.5 - - + +
226A ALA* 3.9 14.1 - - - +
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Residues in contact with VAL 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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74A ALA* 4.0 30.5 - - + +
77A ALA* 4.2 8.5 - - + -
78A ILE* 4.1 8.5 - - + -
90A MET* 5.1 3.4 - - + -
93A LEU* 4.3 14.6 - - + -
94A LYS* 3.9 38.4 + - + -
97A LEU* 4.3 9.0 - - + -
162A ALA 3.7 14.1 - - - +
163A SER* 3.0 8.7 + - - +
165A ILE* 1.3 79.2 - - - +
167A PHE* 1.3 62.6 + - + +
169A ASP* 4.9 2.6 + - - +
170A ASP* 4.5 1.9 - - - +
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Residues in contact with PHE 167 (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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94A LYS* 3.3 49.1 - - + -
97A LEU* 4.0 22.2 - - + -
98A ARG* 3.7 41.7 - - + -
101A ASN* 4.9 0.4 - - - -
163A SER* 3.1 32.0 + - - +
164A SER 4.1 2.7 - - - +
166A VAL* 1.3 78.5 - - + +
168A ALA* 1.3 67.2 + - - +
169A ASP 3.3 2.5 - - - -
170A ASP* 2.8 12.6 + - + +
171A ASP* 2.8 31.4 + - + +
174A TYR* 3.8 29.4 - + + -
175A ALA* 4.2 10.1 - - + -
178A LEU* 4.3 3.1 - - + -
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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