Contacts of the helix formed by residues 157 - 175 (chain D) in PDB entry 3LOC
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 ASP 157 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C GLN* 5.5 6.5 - - - +
199C ASN* 2.9 37.7 + - - +
156D ILE* 1.3 78.2 - - - +
158D PRO* 1.3 71.3 - - + +
159D GLN* 3.4 4.7 - - + +
160D HIS* 3.3 21.8 + - + -
161D LEU 3.3 8.5 + - - -
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Residues in contact with PRO 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D SER* 3.7 41.7 - - - +
144D ILE* 3.8 28.7 - - + -
145D ALA* 3.8 15.5 - - + +
148D VAL* 5.7 0.4 - - + -
156D ILE* 3.5 11.2 - - + +
157D ASP* 1.3 84.7 - - + +
159D GLN* 1.3 65.4 + - + +
161D LEU* 3.2 9.0 + - + +
162D ILE* 2.9 29.9 + - - +
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Residues in contact with GLN 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C VAL* 3.3 35.3 + - + +
183C THR* 3.9 15.4 + - - +
192C PHE* 5.6 1.2 - - - -
137D ILE* 4.9 4.2 - - + +
138D ASP* 4.7 8.1 + - - -
141D SER* 3.7 21.0 - - - +
157D ASP* 3.3 3.8 + - + +
158D PRO* 1.3 76.0 - - + +
160D HIS* 1.3 69.3 + - + +
162D ILE* 3.3 6.8 + - - +
163D PHE* 2.8 53.5 + - + -
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Residues in contact with HIS 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C TYR* 3.0 29.0 + + - +
183C THR* 5.6 0.2 - - - -
192C PHE* 3.7 27.4 - + - -
195C GLN* 4.3 12.1 + - + +
196C THR* 3.4 31.5 + - - +
199C ASN* 3.5 40.1 + - + +
200C VAL* 5.9 0.9 - - + -
203C ILE* 5.0 2.5 - - + -
157D ASP* 3.3 18.8 + - + +
158D PRO 3.2 0.4 - - - -
159D GLN* 1.3 85.9 + - + +
161D LEU* 1.3 65.1 + - - +
163D PHE* 3.2 7.9 + + - +
164D MSE 2.9 27.7 + - + +
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Residues in contact with LEU 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C ILE* 4.1 17.8 - - + +
93D ILE* 3.8 24.9 - - + -
144D ILE* 4.3 25.6 - - + -
153D LEU* 5.0 1.3 - - + -
156D ILE* 4.4 13.2 - - + -
157D ASP 3.3 8.3 + - - +
158D PRO* 3.2 9.3 + - + +
160D HIS* 1.3 77.7 - - - +
162D ILE* 1.3 64.2 + - + +
164D MSE 3.2 4.0 + - + +
165D ILE* 3.0 31.5 + - + +
204D ILE* 3.6 31.0 - - + -
208D ILE* 4.2 19.5 - - + -
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Residues in contact with ILE 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D LEU* 4.5 17.3 - - + -
96D TYR* 4.8 7.4 - - + +
137D ILE* 4.0 26.5 - - + +
140D LYS* 5.2 0.9 - - + -
141D SER* 4.2 9.9 - - - +
144D ILE* 4.1 25.6 - - + -
158D PRO 2.9 18.2 + - - +
159D GLN* 3.5 7.4 - - - +
161D LEU* 1.3 79.6 - - + +
163D PHE* 1.3 65.8 + - + +
165D ILE* 3.1 8.7 + - + +
166D TRP* 2.9 63.9 + - + +
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Residues in contact with PHE 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C HIS* 3.9 19.4 + - + -
172C TYR* 3.6 32.1 - + + +
178C GLN* 5.6 0.9 - - + -
179C VAL* 4.0 35.9 - - + -
182C VAL* 3.6 34.5 - - + -
183C THR* 4.1 7.6 - - - -
137D ILE* 5.5 1.8 - - + -
159D GLN* 2.8 31.4 + - + +
160D HIS* 3.2 9.6 + + - +
162D ILE* 1.3 78.6 - - + +
164D MSE 1.3 59.0 + - - +
166D TRP* 3.2 35.3 + + - +
167D ALA* 2.8 31.7 + - - +
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Residues in contact with MSE 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C MSE 4.1 22.7 - - - +
168C SER* 4.0 22.7 - - - +
172C TYR* 5.1 3.1 + - + +
199C ASN 4.8 0.4 - - - -
200C VAL* 3.7 36.1 - - + +
203C ILE* 3.5 46.4 - - + -
204C ILE* 4.5 7.9 - - - -
160D HIS* 2.9 16.2 + - + +
161D LEU* 3.6 6.1 - - + +
162D ILE 3.2 0.2 - - - -
163D PHE* 1.3 75.5 - - - +
165D ILE* 1.3 58.5 + - - +
167D ALA* 4.3 4.3 - - - -
168D SER* 2.6 35.2 + - - -
203D ILE* 6.2 0.2 - - - -
204D ILE* 4.4 9.2 - - + -
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Residues in contact with ILE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ILE* 3.9 25.6 - - + -
96D TYR* 3.8 42.2 - - + -
97D ILE* 4.2 17.9 - - + -
100D LYS* 4.6 9.0 - - + -
161D LEU* 3.0 34.3 + - + +
162D ILE* 3.1 9.6 + - + +
164D MSE 1.3 74.6 - - - +
166D TRP* 1.3 56.7 + - + +
168D SER* 3.3 4.7 + - - -
169D THR* 2.7 42.3 + - + +
204D ILE* 3.9 19.3 - - + -
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Residues in contact with TRP 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C HIS* 4.5 7.6 - - + -
178C GLN* 3.3 35.2 - - + -
182C VAL* 5.3 1.1 - - + -
77D LEU* 4.3 3.6 - - + -
96D TYR* 2.9 28.6 + + - -
100D LYS* 3.9 5.6 - - - -
133D LEU* 4.3 7.6 - - + -
137D ILE* 3.6 31.6 - - + -
162D ILE* 2.9 34.1 + - + +
163D PHE* 3.4 35.2 - + - +
165D ILE* 1.3 78.5 - - + +
167D ALA* 1.3 57.6 + - - +
169D THR* 3.9 2.2 - - - -
170D GLN* 2.8 49.0 + - - +
212D URA 3.3 46.1 + + + +
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Residues in contact with ALA 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C ALA* 3.5 30.4 - - - +
168C SER* 4.0 7.0 - - - -
171C HIS* 3.6 23.8 + - + +
163D PHE 2.8 20.8 + - - +
164D MSE 3.3 4.0 + - - +
166D TRP* 1.3 73.3 - - - +
168D SER* 1.3 59.2 + - - +
170D GLN* 4.0 2.3 - - - +
171D HIS* 3.0 30.1 + - - +
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Residues in contact with SER 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C MSE 3.8 31.6 - - - -
167C ALA* 3.9 11.4 - - - -
168C SER 5.9 0.2 - - - -
164D MSE 2.6 25.1 + - - -
165D ILE* 3.3 6.6 + - - -
167D ALA* 1.3 77.8 - - - +
169D THR* 1.3 60.1 + - - +
171D HIS* 3.6 3.1 - - - +
172D TYR* 3.2 31.0 - - - -
200D VAL* 4.0 12.5 - - - +
204D ILE* 3.9 9.9 - - - +
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Residues in contact with THR 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ILE* 3.8 31.0 - - + +
100D LYS* 3.5 35.1 - - + -
101D LEU* 3.8 26.0 - - + +
104D SER* 2.6 26.9 + - - -
165D ILE* 2.7 27.1 + - + +
166D TRP 3.4 2.9 + - - -
168D SER* 1.3 79.3 - - - +
170D GLN* 1.3 60.4 + - - +
171D HIS 3.2 2.2 + - - -
172D TYR 3.7 6.4 + - - -
200D VAL* 4.5 3.4 - - + -
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Residues in contact with GLN 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C HIS* 5.4 0.8 - - - -
175C PHE* 3.7 19.0 - - + -
76D TRP* 3.6 25.7 - - + +
100D LYS* 2.6 31.6 + - - +
104D SER* 3.7 7.2 - - - +
111D SER* 4.0 5.4 - - - +
166D TRP* 2.8 28.9 + - - +
167D ALA* 4.4 2.0 - - - +
169D THR* 1.3 75.9 + - - +
171D HIS* 1.3 64.9 + - - +
173D ALA* 3.1 4.0 + - - +
174D ASP* 3.0 38.2 + - - +
212D URA 2.7 37.8 + - - -
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Residues in contact with HIS 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C PHE* 4.0 37.2 - - + +
166C TRP* 4.6 7.4 - - + -
167C ALA* 3.6 24.5 - - + +
170C GLN* 5.4 0.7 - - - -
212C URA 4.9 0.2 - - - -
167D ALA 3.0 20.2 + - - +
168D SER 3.6 9.9 - - - +
169D THR 3.2 0.2 - - - -
170D GLN* 1.3 77.4 - - - +
172D TYR* 1.3 62.9 + + + +
174D ASP* 4.8 0.4 - - - -
175D PHE* 2.8 78.3 + + + +
178D GLN* 4.4 9.2 + - - -
179D VAL* 4.2 14.8 - - + +
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Residues in contact with TYR 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C HIS* 2.8 39.3 + + - +
163C PHE* 3.7 29.9 - + + +
101D LEU* 4.0 8.3 - - + -
168D SER* 3.2 25.4 - - - -
169D THR 3.7 3.6 + - - +
170D GLN 3.2 1.2 - - - -
171D HIS* 1.3 81.8 - + - +
173D ALA* 1.3 60.5 + - - +
176D ALA* 3.4 20.6 - - - +
179D VAL* 4.1 24.1 - - + +
187D LEU* 3.7 34.6 - - + +
192D PHE* 4.4 2.2 - + - -
196D THR* 3.4 34.7 - - + +
200D VAL* 4.6 8.6 - - + +
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Residues in contact with ALA 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D SER* 3.7 31.2 + - - +
108D PRO* 4.0 17.7 - - + +
111D SER* 4.0 12.8 - - - +
112D ARG* 4.4 12.6 + - - -
169D THR 4.4 1.6 + - - -
170D GLN 3.1 6.4 + - - +
172D TYR* 1.3 76.0 - - - +
174D ASP* 1.3 75.4 + - - +
176D ALA* 3.2 19.9 + - - +
177D PRO* 4.7 0.5 - - - +
187D LEU* 5.4 0.4 - - - -
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Residues in contact with ASP 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C MSE 3.5 23.6 - - - +
119C LEU* 3.7 24.2 - - + +
175C PHE* 4.2 7.8 - - - -
111D SER* 2.7 35.4 + - - +
112D ARG* 3.7 5.1 + - - -
115D CYS* 3.5 30.0 - - - +
170D GLN* 3.0 24.1 + - - +
171D HIS* 4.8 0.2 - - - -
173D ALA* 1.3 77.3 - - - +
175D PHE* 1.3 73.5 + - + +
176D ALA 3.4 0.9 + - - -
177D PRO* 4.3 0.5 - - - +
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Residues in contact with PHE 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C PHE* 4.0 7.9 - + - -
115C CYS* 3.8 34.8 - - + -
118C MSE 3.6 24.7 - - + -
170C GLN* 3.7 19.1 - - + -
174C ASP* 4.1 7.4 - - - -
175C PHE* 6.5 0.4 - + - -
212C URA 3.7 15.0 - - - -
115D CYS* 5.8 0.2 - - - -
171D HIS* 2.8 53.9 + + + +
174D ASP* 1.3 85.6 - - + +
176D ALA* 1.3 63.5 - - - +
177D PRO* 3.2 6.3 - - - -
178D GLN* 3.0 35.0 + - + +
179D VAL* 3.0 12.0 + - - +
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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