Contacts of the helix formed by residues 147 - 166 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8K PHE* 4.0 0.7 - - - -
9K GLN* 4.2 3.8 - - - +
145K ASP 3.6 2.7 + - - -
146K LEU* 1.3 75.1 - - - +
148K VAL* 1.3 55.2 + - - +
149K GLU* 3.0 11.8 + - - +
150K ASP* 3.0 35.4 + - - +
151K ALA* 2.7 31.2 + - - +
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Residues in contact with VAL 148 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K PHE* 3.7 20.9 - - + -
9K GLN* 4.6 4.8 - - - +
10K GLY* 4.1 9.4 - - - -
13K ILE* 4.5 0.3 - - - +
147K SER* 1.3 73.6 - - - +
149K GLU* 1.3 61.1 + - - +
151K ALA* 4.0 0.7 - - - +
152K LEU* 3.2 34.9 + - + +
177K HIS* 3.4 48.2 - - + +
187K HIS* 5.3 2.7 - - + +
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Residues in contact with GLU 149 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147K SER* 3.0 8.8 + - - +
148K VAL* 1.3 78.4 - - - +
150K ASP* 1.3 74.7 + - - +
152K LEU* 3.5 10.4 + - - +
153K TYR* 3.2 18.9 + - - +
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Residues in contact with ASP 150 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146K LEU* 4.4 11.1 - - + +
147K SER* 3.0 28.7 + - - +
149K GLU* 1.3 85.2 - - - +
151K ALA* 1.3 61.6 + - - +
153K TYR* 2.9 10.7 + - - +
154K LEU* 2.8 28.7 + - - +
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Residues in contact with ALA 151 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K PHE* 3.5 15.8 - - + -
8K PHE* 3.6 28.7 - - + -
13K ILE* 3.6 18.5 - - + +
146K LEU* 4.1 16.4 - - + +
147K SER 2.7 20.8 + - - +
148K VAL 4.1 0.4 - - - +
150K ASP* 1.3 72.2 - - - +
152K LEU* 1.3 63.3 + - - +
154K LEU* 3.1 4.3 + - - +
155K GLY 3.0 18.5 + - - -
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Residues in contact with LEU 152 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K ILE* 3.5 22.9 - - + +
148K VAL* 3.2 30.0 + - + +
149K GLU* 3.6 8.3 - - - +
150K ASP 3.2 0.2 - - - -
151K ALA* 1.3 78.7 - - - +
153K TYR* 1.3 62.0 + - - +
155K GLY 3.6 0.5 + - - -
156K LYS* 3.2 22.8 + - - +
175K LEU* 3.6 32.6 - - + +
176K TYR 4.1 6.7 - - - +
177K HIS* 4.5 0.9 - - + -
187K HIS* 3.4 55.2 - - + +
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Residues in contact with TYR 153 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K GLU 3.2 9.8 + - - +
150K ASP* 2.9 12.4 + - - +
152K LEU* 1.3 78.7 - - - +
154K LEU* 1.3 57.6 + - - +
156K LYS* 3.1 28.4 + - + +
157K ARG* 2.7 53.8 + - + +
195K LEU* 5.9 0.2 - - + -
199K VAL* 3.5 24.5 - - + +
203K GLU* 2.6 33.9 + - - +
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Residues in contact with LEU 154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K PHE* 4.4 8.5 - - + -
137K VAL* 3.8 22.7 - - + +
138K LEU* 3.8 17.3 - - + -
141K ASN* 3.6 26.2 - - + +
142K TYR* 3.9 25.6 - - + +
146K LEU* 3.6 25.6 - - + -
150K ASP 2.8 12.8 + - - +
151K ALA* 3.1 9.8 + - - +
153K TYR* 1.3 77.5 - - - +
155K GLY* 1.3 58.4 + - - +
157K ARG* 3.3 5.1 + - + +
158K SER* 2.9 34.9 + - - +
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Residues in contact with GLY 155 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K LEU* 4.1 13.2 - - - +
6K PHE* 4.3 8.7 - - - -
13K ILE* 4.5 3.4 - - - -
15K ALA* 4.0 17.3 - - - -
151K ALA 3.0 12.1 + - - -
152K LEU 4.0 2.5 - - - -
154K LEU* 1.3 77.2 - - - +
156K LYS* 1.3 63.7 + - - +
158K SER* 2.9 15.6 + - - -
159K ILE* 3.0 15.4 + - - +
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Residues in contact with LYS 156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152K LEU 3.2 13.5 + - - +
153K TYR* 3.1 28.3 + - + +
155K GLY* 1.3 74.4 - - - +
157K ARG* 1.3 62.0 + - - +
159K ILE* 3.4 3.1 + - - +
160K LEU* 3.0 21.0 + - - +
173K VAL* 4.2 22.1 - - + +
175K LEU* 4.0 25.0 - - + +
190K HIS* 4.1 22.9 + - + -
195K LEU* 3.5 41.4 - - + +
198K LYS* 5.4 8.9 - - - +
199K VAL* 5.6 0.2 - - + -
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Residues in contact with ARG 157 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137K VAL* 4.3 15.3 - - + +
153K TYR* 2.7 37.0 + - + +
154K LEU* 3.6 7.9 - - + +
156K LYS* 1.3 74.1 - - - +
158K SER* 1.3 58.0 + - - +
160K LEU* 3.1 9.2 + - - +
161K ALA* 2.9 45.9 + - - +
199K VAL* 3.6 19.0 - - - +
203K GLU* 2.6 30.4 + - - +
205K SER* 3.7 3.4 + - - -
206K PHE* 3.3 29.9 - - - -
136X SER 5.0 2.0 + - - -
140X HIS* 2.9 39.9 + - + +
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Residues in contact with SER 158 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K LEU* 4.2 7.6 - - - -
134K ALA* 3.7 23.6 - - - +
137K VAL* 2.9 29.9 - - - +
138K LEU* 2.8 34.1 - - - +
154K LEU 2.9 12.3 + - - -
155K GLY 3.4 4.3 - - - -
157K ARG* 1.3 74.9 - - - +
159K ILE* 1.3 65.0 + - - +
161K ALA* 3.3 5.2 + - - +
162K ALA 3.2 15.1 + - - -
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Residues in contact with ILE 159 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K THR* 3.5 32.3 - - + +
4K LEU* 3.1 32.8 - - + -
15K ALA* 3.5 32.1 - - + +
16K VAL* 3.9 11.0 - - - +
17K ASP* 4.0 16.4 - - + -
155K GLY 3.0 6.8 + - - +
156K LYS 3.9 6.1 - - - +
158K SER* 1.3 75.9 - - - +
160K LEU* 1.3 58.0 + - - +
162K ALA* 3.1 5.0 + - - +
163K ALA* 2.8 31.3 + - + +
173K VAL* 3.8 23.6 - - + -
192K VAL* 5.7 0.2 - - + -
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Residues in contact with LEU 160 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156K LYS 3.0 15.1 + - - +
157K ARG* 3.1 14.3 + - - +
159K ILE* 1.3 77.6 - - - +
161K ALA* 1.3 63.2 + - - +
163K ALA* 3.3 3.4 + - - +
164K HIS* 3.0 23.9 + - + +
173K VAL* 4.9 2.0 - - - +
192K VAL* 3.8 26.2 - - + -
195K LEU* 4.2 15.5 - - + -
196K PHE* 4.1 27.6 - - + +
199K VAL* 3.6 43.3 - - + -
206K PHE* 4.0 18.8 - - + -
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Residues in contact with ALA 161 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133K PHE* 4.1 5.5 - - - +
137K VAL* 3.4 28.9 - - + -
157K ARG* 2.9 18.3 + - - +
158K SER 3.4 9.6 - - - +
159K ILE 3.2 0.2 - - - -
160K LEU* 1.3 76.6 - - - +
162K ALA* 1.3 61.3 + - - +
164K HIS* 3.5 3.8 + - - +
165K ARG* 3.4 23.7 + - - +
206K PHE* 4.5 8.5 - - + -
136X SER* 3.9 19.0 - - - +
139X ASP* 5.2 1.7 - - + +
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Residues in contact with ALA 162 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K THR* 3.2 39.0 - - + +
130K GLY* 3.6 13.7 - - - +
133K PHE* 3.6 13.0 - - + +
134K ALA 4.4 0.7 - - - +
158K SER 3.2 6.5 + - - +
159K ILE 3.1 8.4 + - - +
161K ALA* 1.3 76.7 - - - +
163K ALA* 1.3 61.1 + - - +
164K HIS 3.1 2.1 + - - -
165K ARG 3.2 0.5 + - - -
166K ASP* 2.8 36.0 + - - +
169K SER* 4.3 0.4 - - - -
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Residues in contact with ALA 163 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159K ILE* 2.8 24.0 + - + +
160K LEU* 3.8 5.6 - - - +
162K ALA* 1.3 73.0 - - - +
164K HIS* 1.3 62.5 + - - +
166K ASP 3.5 3.3 - - - +
169K SER* 3.3 21.7 - - - +
170K GLY* 3.7 23.6 - - - +
192K VAL* 3.9 25.1 - - + -
194W ASP* 3.2 20.7 - - - +
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Residues in contact with HIS 164 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160K LEU* 3.0 16.9 + - + +
161K ALA 3.6 4.7 - - - +
163K ALA* 1.3 80.3 - - - +
165K ARG* 1.3 63.9 + - + +
166K ASP 5.0 0.5 - - - +
196K PHE* 3.8 15.3 - + + -
206K PHE* 3.4 34.9 - + + -
208K ASN* 6.1 0.4 + - - -
209K VAL* 3.8 25.7 - - + +
29W ASN* 5.4 1.3 + - + -
171W TRP* 3.1 55.6 + + - -
193W GLN* 2.9 31.0 + - + +
194W ASP* 4.5 2.7 - - - -
139X ASP* 3.5 21.5 + - - -
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Residues in contact with ARG 165 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133K PHE* 3.5 38.1 - - + -
161K ALA 3.4 8.6 + - - +
162K ALA 3.2 2.2 + - - -
164K HIS* 1.3 83.0 - - + +
166K ASP* 1.3 62.1 + - - +
167K ALA* 3.4 1.0 + - - -
208K ASN* 5.5 5.1 - - - +
19W ARG* 5.0 0.3 + - - -
24W SER 3.2 4.2 - - - +
25W LEU* 3.9 1.8 - - + -
26W GLY* 2.8 56.9 + - - -
27W VAL* 4.2 9.9 + - - +
171W TRP* 3.9 17.4 - - - -
124X TYR* 3.6 20.8 + - - -
135X PHE* 3.5 34.9 - - + +
136X SER* 5.3 0.4 - - - +
139X ASP* 2.9 42.5 + - - +
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Residues in contact with ASP 166 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129K SER* 2.6 38.4 + - - +
130K GLY* 3.1 15.4 + - - -
133K PHE* 4.1 8.0 - - + -
162K ALA 2.8 20.5 + - - +
163K ALA 3.5 5.7 - - - +
164K HIS 5.1 0.4 - - - -
165K ARG* 1.3 71.2 - - - +
167K ALA* 1.3 67.1 + - - +
168K TYR* 3.1 10.8 + - - +
169K SER* 2.8 39.0 + - - +
24W SER* 3.6 20.7 + - - -
194W ASP 4.1 1.0 - - - +
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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