Contacts of the helix formed by residues 164 - 181 (chain D) in PDB entry 1IB1
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 HIS 164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D GLU* 3.2 28.9 + - + +
160D MET* 3.7 23.1 - - + -
161D GLN* 2.8 24.5 + - - +
162D PRO 3.3 0.4 - - - -
163D THR* 1.3 76.4 + - - +
165D PRO* 1.4 87.5 - - + +
166D ILE* 3.1 34.4 + - + +
167D ARG* 3.0 11.0 + - + +
168D LEU* 2.8 30.5 + - - +
211D TYR* 3.3 34.9 + + + -
89H ARG* 6.1 2.2 - - - -
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Residues in contact with PRO 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D THR 3.3 1.5 - - - +
164D HIS* 1.4 95.7 - - + +
166D ILE* 1.3 57.3 + - + +
168D LEU* 4.5 0.2 - - + -
169D GLY* 3.0 23.0 + - - -
211D TYR* 3.4 30.1 - - + -
213D ASP* 4.3 1.1 - - + -
214D SER* 3.9 15.0 - - - -
217D ILE* 3.4 27.3 - - + +
32H LEU* 5.1 1.0 - - - +
87H GLU 5.2 1.6 - - - +
89H ARG* 3.9 34.8 - - + -
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Residues in contact with ILE 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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41D ARG* 4.1 7.9 - - - +
113D GLU* 3.4 39.0 - - + +
116D VAL* 3.5 30.2 - - + +
117D PHE* 4.0 35.4 - - + +
120D LYS* 4.5 6.7 - - + +
156D SER* 4.8 0.2 + - - -
160D MET* 4.3 2.7 - - - -
164D HIS* 3.1 16.3 + - + +
165D PRO* 1.3 77.1 - - + +
167D ARG* 1.3 67.2 + - - +
169D GLY* 3.9 0.8 - - - -
170D LEU* 3.1 23.0 + - - +
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Residues in contact with ARG 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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153D PHE* 6.0 2.5 - - + -
156D SER* 3.5 36.8 + - - +
157D LYS* 4.1 33.1 + - - +
160D MET* 2.8 39.2 + - + -
161D GLN 3.3 18.8 - - - +
162D PRO* 3.4 30.4 + - - +
164D HIS* 3.0 14.4 + - + +
166D ILE* 1.3 78.8 - - - +
168D LEU* 1.3 64.4 + - + +
170D LEU* 3.3 5.7 + - - +
171D ALA* 3.1 19.8 + - + +
198D GLU* 3.2 28.9 + - - -
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Residues in contact with LEU 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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162D PRO 3.0 27.6 - - - +
163D THR* 3.7 11.9 - - - +
164D HIS 2.8 10.6 + - - +
165D PRO* 4.1 3.4 - - + +
167D ARG* 1.3 78.2 - - + +
169D GLY* 1.3 64.1 + - - +
171D ALA* 3.1 14.4 + - + +
172D LEU* 3.1 10.7 + - - +
195D ALA* 4.0 31.6 - - + +
199D ALA* 4.3 4.5 - - + -
214D SER* 3.5 28.3 - - - +
217D ILE* 3.7 18.2 - - + +
218D MET* 3.9 18.8 - - + -
221D LEU* 4.3 13.8 - - + +
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Residues in contact with GLY 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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120D LYS* 3.9 8.5 - - - -
165D PRO 3.0 19.8 + - - -
166D ILE* 3.4 2.0 + - - -
167D ARG 3.4 0.4 - - - -
168D LEU* 1.3 76.0 - - - +
170D LEU* 1.3 63.3 + - - +
172D LEU* 3.2 5.4 + - - +
173D ASN* 3.1 27.0 + - - +
217D ILE* 3.8 4.4 - - - +
32H LEU* 3.8 25.8 - - - -
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Residues in contact with LEU 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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116D VAL* 3.8 4.3 - - + -
120D LYS* 3.6 29.4 - - + +
149D TYR* 3.7 34.3 - - + +
152D ALA* 3.5 20.0 - - + +
153D PHE* 3.4 43.5 - - + +
156D SER* 3.8 13.0 - - - +
166D ILE 3.1 11.8 + - - +
167D ARG 3.4 7.4 - - - +
169D GLY* 1.3 72.9 - - - +
171D ALA* 1.3 57.7 + - - +
173D ASN* 4.7 0.7 - - - +
174D PHE* 2.8 41.9 + - + +
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Residues in contact with ALA 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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153D PHE* 5.2 4.9 - - + -
167D ARG* 3.1 11.9 + - + +
168D LEU* 3.1 14.5 + - - +
170D LEU* 1.3 76.0 - - - +
172D LEU* 1.3 57.3 + - - +
174D PHE* 4.6 0.2 - - - -
175D SER* 2.9 34.3 + - - -
191D LEU* 3.7 18.5 - - + +
195D ALA* 3.5 32.1 - - + -
221D LEU* 4.4 7.9 - - + -
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Residues in contact with LEU 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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168D LEU 3.1 7.8 + - - +
169D GLY* 3.2 8.5 + - - +
171D ALA* 1.3 78.2 - - - +
173D ASN* 1.3 62.6 + - - +
175D SER* 2.8 20.6 + - - +
176D VAL* 3.1 15.1 + - - +
217D ILE* 4.5 10.5 - - + +
220D LEU* 3.7 37.0 - - + +
221D LEU* 3.8 32.6 - - + +
224D ASN* 3.2 31.2 - - - +
30H HIS 3.6 9.4 - - - +
31H TPO 3.8 18.8 - - - +
32H LEU* 3.8 5.8 - - + +
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Residues in contact with ASN 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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49D LYS* 4.3 0.6 - - - +
120D LYS* 3.5 14.9 - - - +
124D ASP* 2.8 39.5 + - - +
127D ARG* 4.1 6.2 + - - +
149D TYR* 3.9 13.5 + - + +
169D GLY 3.1 12.5 + - - +
170D LEU 4.2 1.8 - - - +
172D LEU* 1.3 75.0 - - - +
174D PHE* 1.3 57.5 + - - +
176D VAL* 3.3 7.8 + - - +
177D PHE* 2.9 27.5 + - - +
31H TPO 3.4 16.6 + - - -
32H LEU* 2.7 36.5 + - - +
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Residues in contact with PHE 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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146D GLN* 4.1 7.0 - - + -
149D TYR* 3.2 57.4 - + + -
150D GLN* 3.5 30.7 - - - -
153D PHE* 4.0 27.4 - + + -
170D LEU* 2.8 26.9 + - + +
171D ALA 3.9 2.2 - - - +
173D ASN* 1.3 73.5 - - - +
175D SER* 1.3 61.9 + - - +
177D PHE* 3.2 14.6 + + - +
178D TYR* 3.1 48.9 + + - -
191D LEU* 4.2 13.5 - - + -
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Residues in contact with SER 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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171D ALA 2.9 16.4 + - - -
172D LEU* 2.8 22.5 + - - +
174D PHE* 1.3 73.2 - - - +
176D VAL* 1.3 59.9 + - - +
178D TYR* 3.2 2.2 + - - -
179D TYR* 2.8 24.4 + - - +
188D ALA* 3.2 38.3 - - - +
191D LEU* 3.7 15.2 - - - +
192D ALA* 4.0 14.9 - - - +
221D LEU* 4.6 0.9 - - - +
224D ASN* 5.1 0.2 + - - -
228D TRP* 4.1 10.7 - - - -
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Residues in contact with VAL 176 (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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127D ARG* 4.6 5.4 - - - +
172D LEU 3.1 15.4 + - - +
173D ASN 3.6 7.4 - - - +
175D SER* 1.3 74.4 - - - +
177D PHE* 1.3 59.7 + - - +
179D TYR* 4.2 6.1 - - + -
180D GLU* 2.9 36.8 + - + +
224D ASN* 3.7 13.2 - - - +
228D TRP* 3.9 10.5 - - + -
29H ARG* 3.4 42.2 - - - +
30H HIS 3.1 27.4 - - - +
31H TPO 3.8 8.5 - - + -
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Residues in contact with PHE 177 (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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127D ARG* 3.7 17.7 - - + +
142D VAL* 3.4 32.8 - - + -
145D SER* 3.4 28.5 - - - -
146D GLN* 3.6 27.4 - - + -
149D TYR* 3.7 13.5 - + + -
173D ASN 2.9 13.0 + - - +
174D PHE* 3.2 26.0 - + - +
176D VAL* 1.3 75.8 - - - +
178D TYR* 1.3 62.4 + + - +
181D ILE* 2.9 57.5 + - + +
182D LEU* 3.0 28.2 + - + -
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Residues in contact with TYR 178 (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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146D GLN* 3.6 15.7 + - - +
150D GLN* 3.9 8.5 + - - -
174D PHE* 3.1 57.0 + + - -
175D SER* 3.5 7.6 - - - +
176D VAL 3.2 0.2 - - - -
177D PHE* 1.3 80.9 - + - +
179D TYR* 1.3 57.4 + - - +
182D LEU* 3.4 31.5 - - + +
183D ASN 3.0 11.3 + - - -
184D SER* 2.8 32.9 + - - +
187D LYS* 4.1 39.5 - - + -
188D ALA* 3.8 14.8 - - + +
191D LEU* 4.0 21.3 - - + -
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Residues in contact with TYR 179 (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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175D SER 2.8 16.6 + - - +
176D VAL* 3.1 4.5 + - + +
178D TYR* 1.3 80.2 - - - +
180D GLU* 1.3 66.9 + - + +
183D ASN* 3.4 17.5 - - - +
184D SER 3.9 2.1 + - - +
185D PRO* 3.7 41.0 - - + +
188D ALA* 3.6 8.9 - - + +
228D TRP* 3.5 69.8 - + + +
29H ARG* 5.5 6.1 - - + -
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Residues in contact with GLU 180 (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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127D ARG* 4.9 1.6 + - - -
131D GLU* 3.8 15.1 - - - +
176D VAL* 2.9 22.8 + - + +
179D TYR* 1.3 80.9 - - + +
181D ILE* 1.3 82.6 + - + +
182D LEU 3.5 0.4 - - - -
183D ASN* 3.6 13.2 + - - +
28H ARG* 4.8 3.6 + - - -
29H ARG* 2.9 47.8 + - - +
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Residues in contact with ILE 181 (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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127D ARG* 3.7 32.1 - - + +
130D ALA* 4.2 11.0 - - + +
131D GLU* 4.3 24.5 - - + +
138D LYS* 3.6 21.5 + - - +
142D VAL* 3.9 23.3 - - + -
177D PHE* 2.9 41.3 + - + +
180D GLU* 1.3 95.7 - - + +
182D LEU* 1.3 62.4 + - - +
183D ASN* 3.6 6.7 + - - -
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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