Contacts of the helix formed by residues 154 - 170 (chain C) in PDB entry 5T0I
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 LEU 154 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ILE* 4.0 14.8 - - + -
152C GLY* 3.2 9.6 - - - +
153C GLY* 1.3 79.8 - - - +
155C ASP* 1.3 50.8 + - - +
156C LYS* 3.1 3.4 - - - -
157C GLN* 2.5 55.4 + - + +
158C ILE* 2.7 29.7 + - + -
188C LEU* 5.6 1.8 - - + -
194C THR 5.6 1.6 - - - +
195C GLY* 3.7 25.1 - - - +
196C LYS* 4.8 2.7 - - - +
199C LEU* 3.7 23.8 - - + -
317C PHE* 5.5 5.6 - - + -
318C PRO* 4.0 21.1 - - + -
324C ALA* 5.7 4.5 - - + -
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Residues in contact with ASP 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C GLY* 5.7 0.2 - - - -
153C GLY* 3.6 17.4 - - - +
154C LEU* 1.3 74.7 - - - +
156C LYS* 1.3 80.6 + - - +
158C ILE* 3.2 34.1 - - + +
159C LYS* 3.3 11.4 + - - +
323C GLU* 5.4 6.1 - - - +
327C ASP* 5.7 0.9 - - - -
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Residues in contact with LYS 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ARG* 4.2 23.8 + - - +
153C GLY 5.9 0.4 - - - +
154C LEU 3.1 0.6 - - - -
155C ASP* 1.3 98.3 + - - +
157C GLN* 1.3 64.8 + - + +
159C LYS* 3.7 6.0 + - - +
160C GLU* 3.4 25.3 + - - +
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Residues in contact with GLN 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C LEU* 2.5 42.2 + - + +
156C LYS* 1.3 73.9 - - + +
158C ILE* 1.3 58.8 + - - +
159C LYS 3.2 1.8 - - - -
160C GLU* 2.9 18.3 + - - +
161C ILE* 2.9 29.5 + - - +
188C LEU* 5.0 4.2 - - - +
199C LEU* 5.3 5.4 - - + +
315C ILE* 3.6 25.7 - - + +
316C GLU 2.3 38.4 + - - +
317C PHE* 4.6 0.7 - - - -
318C PRO* 3.3 19.1 - - - +
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Residues in contact with ILE 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C TYR* 4.3 23.1 - - + +
151C ILE* 5.5 3.6 - - + -
154C LEU* 2.7 33.3 + - + +
155C ASP* 3.2 24.0 - - + +
157C GLN* 1.3 71.9 - - - +
159C LYS* 1.3 60.5 + - - +
161C ILE* 3.4 11.4 - - + +
162C LYS* 2.8 50.3 + - - +
199C LEU* 3.7 29.4 - - + -
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Residues in contact with LYS 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B LEU 4.6 0.2 + - - -
408B ARG* 3.6 46.4 - - - +
410B ARG* 3.3 40.9 - - - +
155C ASP 3.3 11.8 + - - +
156C LYS* 3.9 7.2 - - - +
157C GLN 3.2 0.8 - - - -
158C ILE* 1.3 82.2 - - - +
160C GLU* 1.3 58.6 + - - +
162C LYS* 3.4 18.2 - - - +
163C GLU* 2.6 53.9 + - - +
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Residues in contact with GLU 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ARG* 4.5 14.6 + - - +
156C LYS* 3.4 18.2 - - - +
157C GLN* 2.9 17.4 + - - +
159C LYS* 1.3 80.5 - - - +
161C ILE* 1.3 61.3 + - - +
162C LYS 3.7 0.2 + - - -
163C GLU* 4.3 6.1 + - - +
164C VAL 4.4 2.6 + - - -
313C ARG* 2.9 50.2 + - - +
314C LYS 3.1 20.1 - - - +
315C ILE* 3.2 18.2 - - + +
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Residues in contact with ILE 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C GLN 2.9 15.2 + - - +
158C ILE* 3.4 19.3 - - + +
160C GLU* 1.3 78.8 - - - +
162C LYS* 1.3 68.3 + - - +
164C VAL* 3.1 11.0 + - + -
165C ILE* 2.9 40.9 + - + +
186C VAL* 3.6 44.2 - - + -
188C LEU* 5.7 2.5 - - + -
199C LEU* 4.5 11.2 - - + -
203C VAL* 4.0 21.5 - - + -
292C ILE* 5.5 6.7 - - + -
313C ARG* 4.8 0.7 - - + -
315C ILE* 4.3 7.2 - - + -
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Residues in contact with LYS 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C TYR* 3.2 28.3 - - + +
158C ILE* 2.8 59.3 + - - +
159C LYS* 3.4 21.2 - - - +
160C GLU 3.5 0.2 - - - -
161C ILE* 1.3 76.5 - - - +
163C GLU* 1.3 62.1 + - - +
165C ILE* 2.7 9.9 + - - +
166C GLU* 2.4 56.1 + - + +
203C VAL* 3.8 9.2 - - + -
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Residues in contact with GLU 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B LEU* 5.1 8.5 - - + -
407B LEU* 3.6 38.2 - - + +
408B ARG* 5.7 1.6 - - - -
410B ARG* 4.9 5.4 + - - -
159C LYS* 2.6 57.3 + - - +
160C GLU 4.7 4.7 - - - +
161C ILE 3.4 0.8 - - - -
162C LYS* 1.3 81.8 - - - +
164C VAL* 1.3 57.5 + - - +
166C GLU* 4.3 4.5 - - - +
167C LEU* 3.2 34.2 - - + +
171C HIS* 6.1 2.9 - - + +
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Residues in contact with VAL 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B LEU* 5.0 6.3 - - + -
160C GLU 4.4 0.6 + - - -
161C ILE* 3.1 16.6 + - + +
162C LYS 3.0 0.8 - - - -
163C GLU* 1.3 78.3 - - - +
165C ILE* 1.3 69.5 + - + +
167C LEU* 5.0 0.7 - - - -
168C PRO* 3.2 9.9 - - - +
183C PRO* 3.7 33.8 - - + +
185C GLY* 5.3 5.2 - - - +
186C VAL* 5.3 4.0 - - + -
290C LYS* 2.3 34.2 + - + +
313C ARG* 3.6 42.2 - - + +
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Residues in contact with ILE 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C ILE* 3.1 40.4 - - + +
162C LYS 2.7 10.0 + - - +
164C VAL* 1.3 77.9 - - + +
166C GLU* 1.3 62.9 + - - +
167C LEU 3.4 0.2 + - - -
168C PRO* 3.6 2.3 - - - +
169C VAL* 3.6 11.9 - - + +
186C VAL* 5.4 1.6 - - + -
203C VAL* 4.1 26.5 - - + +
204C ALA* 5.2 1.1 - - + +
207C THR* 4.2 15.5 - - + +
209C CYS* 4.9 3.6 - - - -
245C ILE* 4.8 17.0 - - + -
290C LYS* 3.4 45.1 - - + +
291C VAL 5.5 0.4 - - - +
292C ILE* 5.3 8.7 - - + -
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Residues in contact with GLU 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C TYR* 4.8 1.4 + - - -
162C LYS* 2.4 56.5 + - + +
163C GLU* 4.7 2.2 - - - +
165C ILE 1.3 66.8 - - - -
167C LEU* 1.3 63.3 + - - +
169C VAL* 3.5 2.0 + - - +
170C LYS* 3.3 34.4 + - + +
171C HIS* 3.0 28.0 + - + -
203C VAL* 3.6 14.9 - - - +
206C HIS* 5.0 1.5 - - - +
207C THR* 2.3 46.9 + - - +
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Residues in contact with LEU 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B LEU* 4.6 8.3 - - + -
163C GLU* 3.2 25.1 + - - +
164C VAL* 4.3 0.7 - - - +
166C GLU* 1.3 79.0 - - - +
168C PRO* 1.3 65.6 - - + +
171C HIS* 2.9 49.0 + - + +
172C PRO* 3.0 12.5 - - + -
174C LEU* 3.8 12.3 - - + -
175C PHE* 3.5 43.7 - - + -
178C LEU* 4.2 23.3 - - + -
180C ILE* 5.3 5.2 - - + -
183C PRO* 6.0 1.1 - - + -
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Residues in contact with PRO 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C VAL 3.2 16.6 - - - +
165C ILE 3.6 5.6 - - - +
167C LEU* 1.3 91.1 - - + +
169C VAL* 1.3 58.3 + - - +
172C PRO* 3.1 23.3 - - + +
175C PHE* 4.4 14.1 - - + -
182C GLN* 5.2 4.0 - - + -
183C PRO* 4.7 7.4 - - + -
287C LYS* 3.5 35.4 - - + +
288C ASN* 4.3 9.5 + - - +
290C LYS* 3.3 23.6 - - - +
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Residues in contact with VAL 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C ILE* 3.6 17.7 - - + +
166C GLU 3.5 5.1 + - - +
167C LEU 3.2 1.0 - - - -
168C PRO* 1.3 80.3 - - + +
170C LYS* 1.3 69.0 + - + +
172C PRO* 4.3 1.5 - - - +
207C THR* 3.8 34.5 - - + +
208C ASP* 5.9 0.7 - - + -
209C CYS* 4.6 5.2 - - + -
288C ASN* 3.2 39.9 - - - +
290C LYS* 5.1 0.4 - - - -
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Residues in contact with LYS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C GLU* 3.3 31.1 + - - +
169C VAL* 1.3 87.7 - - + +
171C HIS* 1.3 70.0 + - + +
172C PRO* 3.0 14.2 - - - +
173C GLU* 3.4 8.3 - - - +
206C HIS 4.3 4.2 + - - -
207C THR* 2.9 37.6 + - - +
208C ASP* 4.9 8.7 - - - -
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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