Contacts of the helix formed by residues 147 - 166 (chain L) in PDB entry 3TDD
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 147 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L PHE* 3.6 6.3 - - - -
145L TYR 4.2 0.2 + - - -
146L LEU* 1.3 74.3 - - - +
148L VAL* 1.3 65.9 + - - +
149L GLU* 2.8 23.2 + - - +
150L GLU* 2.9 18.4 + - - +
151L VAL* 2.9 21.1 + - - +
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Residues in contact with VAL 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L PHE* 3.3 37.1 - - + -
13L VAL* 4.6 1.1 - - + -
147L SER* 1.3 71.5 - - - +
149L GLU* 1.3 82.4 + - + +
151L VAL* 4.0 0.8 - - - +
152L ILE* 3.0 42.6 + - + +
177L ILE* 3.9 29.4 - - + -
179L THR* 6.0 2.2 - - + -
185L ARG* 4.3 9.0 - - - +
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Residues in contact with GLU 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147L SER* 2.8 24.2 + - - +
148L VAL* 1.3 96.3 - - + +
150L GLU* 1.3 63.5 + - - +
152L ILE* 3.6 6.8 + - - +
153L LYS* 3.4 29.0 + - - +
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Residues in contact with GLU 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14L LYS* 6.2 0.2 - - - +
146L LEU* 4.0 34.1 - - + -
147L SER* 2.9 17.7 + - - +
149L GLU* 1.3 74.9 - - - +
151L VAL* 1.3 66.0 + - - +
153L LYS* 3.1 36.0 + - - +
154L LEU* 3.2 19.5 + - + +
202V LYS* 3.2 36.1 - - - +
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Residues in contact with VAL 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L ILE* 4.0 30.1 - - + -
11L PHE* 3.6 25.1 - - + -
13L VAL* 3.8 30.1 - - + -
145L TYR* 5.0 3.1 - - + -
146L LEU* 3.8 25.8 - - + -
147L SER 2.9 17.6 + - - +
148L VAL 4.0 4.0 - - - +
150L GLU* 1.3 77.3 - - - +
152L ILE* 1.3 63.7 + - - +
154L LEU* 2.9 9.7 + - - +
155L VAL* 2.9 21.4 + - + +
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Residues in contact with ILE 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L VAL* 4.8 11.0 - - + -
148L VAL* 3.0 38.2 + - + +
149L GLU* 4.0 7.4 - - - +
150L GLU 3.4 0.2 - - - -
151L VAL* 1.3 76.8 - - + +
153L LYS* 1.3 60.5 + - + +
155L VAL* 3.8 7.4 - - + +
156L ARG* 3.1 34.9 + - + +
175L ILE* 4.0 22.2 - - + -
177L ILE* 4.2 12.1 - - + -
185L ARG* 4.7 1.3 - - - +
187L GLU* 3.6 34.1 - - - +
189L TYR* 4.3 3.1 - - - +
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Residues in contact with LYS 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L GLU* 3.4 17.8 + - - +
150L GLU* 3.1 33.9 + - - +
151L VAL 3.0 1.0 - - - -
152L ILE* 1.3 73.8 - - - +
154L LEU* 1.3 64.1 + - + +
156L ARG* 3.4 2.1 + - - +
157L ASP* 2.9 34.8 + - - +
201V GLN* 3.4 48.2 + - + +
202V LYS* 4.9 9.0 - - + +
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Residues in contact with LEU 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L LEU* 5.5 0.2 - - - -
6L ILE* 5.2 4.9 - - + -
137L PHE* 4.0 8.5 - - + -
138L LEU* 5.1 7.2 - - + -
141L GLN* 3.9 20.2 - - + +
142L VAL* 3.7 28.5 - - + -
146L LEU* 3.7 22.4 - - + -
150L GLU* 3.6 24.0 - - - +
151L VAL* 2.9 8.4 + - - +
153L LYS* 1.3 74.9 - - - +
155L VAL* 1.3 58.8 + - - +
157L ASP* 3.7 3.1 - - - +
158L SER* 2.8 35.6 + - - -
202V LYS* 4.5 2.7 - - + -
204V TYR* 3.5 31.4 - - + +
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Residues in contact with VAL 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L LEU* 4.0 22.9 - - + +
6L ILE* 4.0 14.4 - - + -
13L VAL* 4.4 11.7 - - + -
15L ALA* 3.9 19.1 - - + -
151L VAL* 2.9 22.8 + - + +
152L ILE* 3.8 11.2 - - - +
154L LEU* 1.3 76.5 - - - +
156L ARG* 1.3 64.2 + - - +
158L SER* 3.0 5.4 + - - -
159L PHE* 3.0 36.8 + - + -
173L LEU* 4.1 2.7 - - + -
175L ILE* 3.8 24.9 - - + -
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Residues in contact with ARG 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152L ILE* 3.1 28.1 + - + +
153L LYS* 3.8 3.8 - - - +
155L VAL* 1.3 78.4 - - - +
157L ASP* 1.3 62.1 + - - +
159L PHE* 3.3 2.8 + - - +
160L THR* 3.0 30.5 + - + +
173L LEU* 4.0 21.3 - - + +
175L ILE* 4.6 1.6 - - + -
189L TYR* 3.0 59.6 + - + +
198V GLU* 3.7 22.4 + - - -
201V GLN* 3.2 39.2 + - + +
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Residues in contact with ASP 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137L PHE* 4.6 5.8 - - + -
153L LYS 2.9 17.6 + - - +
154L LEU 3.8 3.6 - - - +
156L ARG* 1.3 76.9 - - - +
158L SER* 1.3 63.2 + - - +
160L THR* 3.1 7.4 + - - -
161L SER* 3.0 28.4 + - - -
197V ARG* 4.4 0.6 + - - +
200V LYS* 3.6 13.6 - - + +
201V GLN* 2.7 31.4 + - - +
202V LYS 3.4 12.3 + - - +
204V TYR* 2.4 44.4 + - + +
140W SER* 4.9 2.0 - - - +
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Residues in contact with SER 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L LEU* 4.2 7.0 - - - -
134L ILE* 3.6 27.5 - - - +
137L PHE* 3.3 26.5 - - - -
138L LEU* 3.3 14.4 - - - +
154L LEU 2.8 20.8 + - - -
155L VAL 3.2 10.1 - - - -
157L ASP* 1.3 73.6 - - - +
159L PHE* 1.3 58.2 + - - +
161L SER* 3.7 5.2 - - - -
162L ALA* 2.9 29.4 + - - +
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Residues in contact with PHE 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L THR* 3.5 38.4 - - + -
3L ILE 4.3 1.6 - - - -
4L LEU* 3.8 32.1 - - + -
15L ALA* 4.1 6.3 - - + -
16L GLY* 4.0 11.2 - - - -
17L ASP* 3.6 24.5 - - + -
134L ILE* 4.7 4.7 - - + -
155L VAL* 3.0 30.2 + - + +
156L ARG 3.3 3.6 + - - +
157L ASP 3.2 0.2 - - - -
158L SER* 1.3 79.8 - - - +
160L THR* 1.3 57.0 + - - +
162L ALA* 3.8 4.3 - - + +
163L THR* 2.7 38.6 + - - -
169L VAL* 4.3 10.6 - - + +
173L LEU* 3.8 30.3 - - + -
191L LEU* 4.4 11.2 - - + -
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Residues in contact with THR 160 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156L ARG* 3.0 19.6 + - + +
157L ASP* 3.1 16.0 + - - -
159L PHE* 1.3 73.3 - - - +
161L SER* 1.3 65.3 + - - +
163L THR* 3.5 7.6 + - - -
164L GLU* 3.2 27.5 + - - +
191L LEU* 3.9 15.7 - - + -
197V ARG* 2.7 32.5 + - - +
198V GLU* 3.6 32.8 - - + +
200V LYS* 5.5 0.9 - - - -
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Residues in contact with SER 161 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133L LEU* 5.5 1.1 - - - -
157L ASP 3.0 16.3 + - - -
158L SER* 3.7 4.7 - - - -
160L THR* 1.3 75.0 + - - +
162L ALA* 1.3 66.4 + - - +
164L GLU* 2.9 19.9 + - - +
165L ARG* 3.4 6.1 + - - +
197V ARG* 3.0 20.5 + - - +
200V LYS* 5.0 0.7 - - - +
136W GLY* 4.8 5.4 - - - -
139W GLU* 3.4 25.8 + - - +
140W SER* 2.7 27.5 + - - -
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Residues in contact with ALA 162 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L THR* 5.7 0.2 - - + -
130L ALA* 3.7 26.9 - - + -
133L LEU* 4.4 13.7 - - + +
134L ILE* 4.3 11.9 - - + -
158L SER 2.9 18.3 + - - +
159L PHE* 3.8 7.2 - - + +
161L SER* 1.3 77.6 - - - +
163L THR* 1.3 58.1 + - - +
165L ARG 3.1 1.6 + - - -
166L HIS* 2.9 33.8 + - - +
169L VAL* 4.2 10.3 - - + -
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Residues in contact with THR 163 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159L PHE 2.7 24.7 + - - -
160L THR* 3.7 9.0 - - - -
161L SER 3.2 0.2 - - - -
162L ALA* 1.3 77.2 - - - +
164L GLU* 1.3 60.6 + - - +
165L ARG 3.6 0.2 + - - -
166L HIS 3.7 9.9 - - - +
169L VAL* 3.5 33.6 + - - +
170L GLY* 3.8 8.5 - - - -
191L LEU* 3.8 14.8 - - - +
192L LYS* 3.9 38.7 - - + +
194L ASP* 5.2 5.0 - - - +
19V ARG* 5.3 5.4 + - - -
26V VAL* 5.7 0.7 - - - +
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Residues in contact with GLU 164 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160L THR 3.2 14.9 - - - +
161L SER 2.9 10.0 + - - +
163L THR* 1.3 80.2 - - - +
165L ARG* 1.3 60.9 + - - +
166L HIS 3.7 0.2 - - - -
192L LYS* 2.9 43.7 + - - +
19V ARG* 5.8 0.7 + - - -
26V VAL* 3.6 19.9 - - - +
29V LYS* 3.2 35.8 + - - +
197V ARG* 3.1 30.2 - - + +
139W GLU* 3.6 25.4 - - - +
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Residues in contact with ARG 165 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133L LEU* 3.7 20.2 - - + -
161L SER 3.4 1.7 + - - +
162L ALA 3.1 2.6 + - - -
164L GLU* 1.3 81.5 - - - +
166L HIS* 1.3 59.0 + - - +
25V ILE* 3.3 12.5 - - + +
26V VAL* 2.8 44.1 + - - +
27V ALA 2.9 29.1 + - - -
28V ASP* 4.2 3.2 - - - +
29V LYS* 3.2 29.9 - - - +
123W ASP* 4.3 7.9 + - - -
124W PHE* 3.4 26.7 + - - -
135W PHE* 3.2 38.3 - - + +
139W GLU* 2.7 32.0 + - + +
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Residues in contact with HIS 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129L ALA* 3.4 43.4 + - + +
130L ALA* 4.1 10.2 + - + -
133L LEU* 4.6 4.2 - - + +
162L ALA 2.9 14.5 + - - +
163L THR 3.7 6.4 - - - +
164L GLU 3.7 1.2 - - - -
165L ARG* 1.3 79.8 - - - +
167L ILE* 1.3 64.6 + - - +
168L GLN* 3.1 49.4 + - + +
169L VAL* 3.1 31.7 + - + +
24V PRO* 3.5 28.8 - - + +
25V ILE* 3.8 16.2 - - + +
26V VAL* 4.7 1.6 - - - -
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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
------------------------------------------------------------
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