Contacts of the helix formed by residues 151 - 169 (chain P) in PDB entry 1U8F
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 151 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124P PRO* 3.5 24.8 - - - +
150P ALA* 1.3 77.4 - - - +
152P CYS* 1.3 68.1 + - - +
153P THR* 3.5 4.5 + - - -
154P THR* 3.1 27.1 + - - -
155P ASN* 2.9 24.9 + - - -
213P ALA* 3.9 9.3 - - - +
320P TYR* 3.6 6.5 - - - -
336P NAD 4.8 4.5 - - - -
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Residues in contact with CYS 152 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151P SER* 1.3 76.7 - - - +
153P THR* 1.3 74.3 + - - +
155P ASN* 3.2 6.3 + - - +
156P CYS* 3.1 16.6 + - - +
179P HIS* 3.4 29.6 - - - -
292P SER 4.9 0.5 - - - +
314P TYR* 3.7 18.9 - - + -
316P ASN* 3.7 17.7 - - + +
320P TYR* 3.7 16.6 - - + -
336P NAD 3.7 32.6 - - + -
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Residues in contact with THR 153 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151P SER* 3.2 3.3 + - - -
152P CYS* 1.3 88.8 - - - +
154P THR* 1.3 56.2 + - - +
156P CYS* 3.1 2.8 + - - +
157P LEU* 2.9 26.5 + - - +
175P MET* 3.8 27.8 - - + -
177P THR* 4.1 11.1 - - + +
179P HIS* 3.9 6.6 - - - -
211P THR* 5.1 2.2 + - - +
213P ALA* 3.5 24.5 - - + -
243P VAL* 4.2 4.0 - - + -
314P TYR* 2.7 29.0 + - - +
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Residues in contact with THR 154 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124P PRO* 5.6 1.2 - - - +
132P VAL* 4.0 19.5 - - + -
150P ALA* 4.0 12.5 - - + +
151P SER* 3.1 18.2 + - - -
153P THR* 1.3 76.7 - - - +
155P ASN* 1.3 58.9 + - - +
157P LEU* 4.5 3.1 - - - +
158P ALA* 2.9 33.4 + - + +
213P ALA* 2.9 37.6 + - - +
216P ALA* 3.7 17.8 - - + +
217P VAL* 4.4 11.9 - - + +
220P VAL* 4.8 2.2 - - + -
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Residues in contact with ASN 155 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P VAL* 3.5 29.2 - - - +
133P MET 4.2 3.3 + - - +
149P ASN* 2.9 29.9 + - - +
150P ALA* 3.9 4.9 - - - +
151P SER 2.9 21.7 + - - +
152P CYS* 3.2 11.2 + - - +
154P THR* 1.3 76.9 - - - +
156P CYS* 1.3 57.6 + - - +
159P PRO* 3.0 24.5 - - - +
292P SER* 3.3 22.0 + - - +
320P TYR* 3.4 15.9 - - + -
323P ARG* 4.1 19.4 - - + +
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Residues in contact with CYS 156 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152P CYS 3.1 5.6 + - - +
153P THR 3.1 8.6 + - - +
155P ASN* 1.3 78.7 - - - +
157P LEU* 1.3 63.0 + - - +
159P PRO* 3.5 4.0 - - - +
160P LEU* 4.0 4.9 + - - +
243P VAL* 3.4 18.6 - - + -
292P SER 3.2 13.2 - - - +
293P SER* 2.9 36.1 + - - -
312P SER* 3.6 17.0 - - - -
313P TRP 4.1 0.4 - - - -
314P TYR* 3.4 39.9 - - + -
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Residues in contact with LEU 157 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153P THR 2.9 16.1 + - - +
154P THR* 4.7 1.1 - - - -
156P CYS* 1.3 78.4 - - - +
158P ALA* 1.3 60.8 + - - +
160P LEU* 3.2 7.7 + - + +
161P ALA* 2.8 33.4 + - + +
175P MET* 3.9 22.7 - - + -
213P ALA 4.7 0.4 - - - +
214P ALA* 3.8 23.8 - - + +
217P VAL* 3.5 26.7 - - + -
228P LEU* 4.6 8.1 - - + -
243P VAL* 4.1 18.2 - - + -
245P LEU* 3.9 34.3 - - + -
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Residues in contact with ALA 158 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P VAL* 4.0 9.4 - - + -
135P VAL* 3.9 16.2 - - + -
154P THR 2.9 23.7 + - - +
157P LEU* 1.3 73.2 - - - +
159P PRO* 1.3 62.0 - - + +
162P LYS* 2.8 30.8 + - - +
217P VAL* 4.1 16.0 - - + +
220P VAL* 4.0 22.7 - - + -
221P ILE* 3.7 4.4 - - + +
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Residues in contact with PRO 159 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P VAL* 4.4 5.2 - - + -
135P VAL* 3.9 17.7 - - + -
155P ASN 3.0 30.1 - - - +
156P CYS 3.5 7.4 - - - +
158P ALA* 1.3 92.8 - - + +
160P LEU* 1.3 59.8 + - - +
162P LYS* 3.4 4.7 + - + +
163P VAL* 3.3 26.7 + - - +
270P LEU* 4.1 8.5 - - + +
273P ILE* 3.9 28.5 - - + -
274P LEU* 4.4 17.0 - - + -
292P SER* 4.6 1.1 - - - -
293P SER* 4.6 3.6 - - - -
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Residues in contact with LEU 160 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156P CYS 4.0 9.1 + - - +
157P LEU* 3.2 11.8 + - + +
159P PRO* 1.3 76.4 - - - +
161P ALA* 1.3 68.2 + - - +
163P VAL* 3.1 4.1 + - + -
164P ILE* 3.0 46.1 + - + +
243P VAL* 5.3 3.4 - - + -
245P LEU* 4.7 12.3 - - + -
262P VAL* 4.3 13.5 - - + -
274P LEU* 4.6 10.4 - - + +
293P SER* 4.3 6.1 - - - +
295P PHE* 4.0 25.1 - - + -
310P LEU* 4.1 27.1 - - + +
312P SER* 4.1 21.8 - - - -
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Residues in contact with ALA 161 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157P LEU* 2.8 32.2 + - + +
158P ALA 3.7 3.4 - - - +
160P LEU* 1.3 75.2 - - - +
162P LYS* 1.3 57.1 + - - +
164P ILE* 4.5 1.3 - - - -
165P HIS* 2.8 35.1 + - - +
170P ILE* 3.7 15.0 - - + +
217P VAL* 4.3 10.8 - - + -
221P ILE* 4.4 1.6 - - + -
224P LEU* 4.1 19.7 - - + -
228P LEU* 4.5 3.6 - - + -
245P LEU* 5.0 2.7 - - + -
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Residues in contact with LYS 162 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134P GLY 3.7 24.5 - - - +
135P VAL* 4.2 20.7 + - + +
158P ALA 2.8 18.9 + - - +
159P PRO* 3.5 6.3 - - + +
161P ALA* 1.3 75.9 - - - +
163P VAL* 1.3 60.7 + - + +
165P HIS* 4.0 1.9 - - - +
166P ASP* 2.8 57.9 + - - +
221P ILE* 3.8 16.8 - - + +
270P LEU* 4.9 13.7 - - + -
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Residues in contact with VAL 163 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159P PRO 3.3 12.8 + - - +
160P LEU* 3.1 6.6 + - - +
162P LYS* 1.3 77.7 - - + +
164P ILE* 1.3 62.1 + - - +
166P ASP* 4.0 2.9 - - - +
167P ASN* 2.8 45.5 + - - +
261P VAL* 3.8 30.7 - - + +
262P VAL* 4.1 12.8 - - + -
265P ALA* 3.6 13.9 - - + -
270P LEU* 3.6 24.7 - - + -
274P LEU* 3.7 9.4 - - + -
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Residues in contact with ILE 164 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160P LEU* 3.0 24.3 + - + +
161P ALA* 3.9 3.1 - - - +
163P VAL* 1.3 77.0 - - + +
165P HIS* 1.3 59.1 + - - +
168P PHE* 2.8 43.1 + - + +
169P GLY 3.3 2.6 + - - -
170P ILE* 3.8 14.4 - - + -
245P LEU* 5.5 1.1 - - + -
247P CYS* 4.6 1.8 - - - -
249P LEU* 3.5 31.2 - - + -
258P ILE* 3.9 21.8 - - + -
262P VAL* 4.3 15.0 - - + -
310P LEU* 3.6 33.4 - - + -
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Residues in contact with HIS 165 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161P ALA 2.8 22.8 + - - +
162P LYS* 4.0 3.4 - - - +
164P ILE* 1.3 75.3 - - - +
166P ASP* 1.3 69.5 + - - +
167P ASN 4.2 0.2 - - - -
169P GLY* 2.9 31.2 + - - +
170P ILE* 2.9 38.4 + - + +
221P ILE* 4.7 7.4 - - + -
223P GLU* 2.9 40.8 + - + +
224P LEU* 3.4 30.6 - - + +
227P LYS* 5.7 1.8 - - + -
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Residues in contact with ASP 166 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162P LYS* 2.8 57.2 + - - +
163P VAL* 4.0 5.6 - - - +
165P HIS* 1.3 84.5 - - - +
167P ASN* 1.3 65.2 + - - +
223P GLU* 5.6 0.2 - - - +
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Residues in contact with ASN 167 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163P VAL* 2.8 41.3 + - - +
165P HIS 3.2 0.6 - - - -
166P ASP* 1.3 85.0 - - - +
168P PHE* 1.3 88.0 + - + +
251P LYS* 3.9 15.0 - - - +
261P VAL* 3.6 24.9 + - - +
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Residues in contact with PHE 168 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164P ILE* 2.8 26.7 + - + +
167P ASN* 1.3 89.0 - - + +
169P GLY* 1.3 65.5 - - - +
249P LEU* 4.0 19.3 - - + -
250P GLU* 3.3 3.1 + - - +
251P LYS* 2.9 50.5 + - + +
252P PRO 4.0 9.9 - - - -
253P ALA* 3.4 30.7 - - + -
257P ASP* 3.9 31.2 - - + -
258P ILE* 3.9 14.1 - - + -
261P VAL* 3.7 27.1 - - + -
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Residues in contact with GLY 169 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164P ILE 3.3 3.4 + - - -
165P HIS* 2.9 28.8 + - - -
168P PHE* 1.3 76.5 - - - +
170P ILE* 1.3 63.7 + - - -
171P VAL 3.8 0.2 - - - -
249P LEU* 3.2 7.1 - - - +
250P GLU* 2.9 37.2 + - - -
251P LYS* 6.1 0.7 - - - -
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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
------------------------------------------------------------
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