Contacts of the helix formed by residues 154 - 175 (chain D) in PDB entry 5HP1
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 LYS 154 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LYS* 4.6 3.4 - - - +
81D ASN* 2.6 47.8 + - + +
82D LYS* 5.3 0.4 - - - +
84D THR* 3.2 25.5 + - + -
85D GLN 3.7 11.4 + - - -
86D ASP* 2.8 30.2 + - - +
87D PHE* 4.7 7.3 - - + +
152D GLY 3.9 0.6 + - - -
153D TRP* 1.3 75.4 - - - +
155D GLY* 1.3 64.0 + - - +
157D PRO* 3.4 13.4 - - - +
158D ALA* 4.0 8.1 + - - +
184D MET* 3.7 31.1 - - + -
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Residues in contact with GLY 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D PHE* 3.8 15.9 - - - -
153D TRP* 3.1 36.1 - - - -
154D LYS* 1.3 82.1 - - - +
156D SER* 1.3 63.4 + - - +
158D ALA* 3.4 3.6 - - - +
159D ILE* 3.0 27.4 + - - +
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Residues in contact with SER 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D TYR* 3.6 27.6 - - - -
149D LEU* 3.8 19.0 - - - +
150D PRO* 2.7 25.7 + - - +
153D TRP* 3.1 23.6 + - - -
155D GLY* 1.3 77.2 - - - +
157D PRO* 1.3 66.9 - - - +
159D ILE 3.4 0.2 + - - -
160D PHE* 2.9 26.5 + - - +
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Residues in contact with PRO 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D ILE* 4.2 13.9 - - + -
115D TYR* 3.6 13.7 - - + +
153D TRP 3.2 14.6 - - - +
154D LYS* 3.4 13.9 - - - +
156D SER* 1.3 91.6 - - - +
158D ALA* 1.3 63.4 + - - +
160D PHE* 3.6 0.7 - - + -
161D GLN* 2.9 26.3 + - - +
182D GLN* 3.5 32.3 - - - +
184D MET* 3.7 27.1 - - - +
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Residues in contact with ALA 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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87D PHE* 3.7 38.4 - - + -
92D LEU* 3.4 27.4 - - + +
93D GLY* 5.2 2.5 - - - +
94D ILE* 4.9 3.7 - - - +
154D LYS 4.0 8.7 - - - +
155D GLY 3.4 9.8 + - - +
157D PRO* 1.3 83.3 - - - +
159D ILE* 1.3 62.2 + - - +
161D GLN* 3.2 17.0 + - - +
162D SER 4.7 0.2 + - - -
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Residues in contact with ILE 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 4.1 35.1 - - + +
10D VAL* 3.7 29.4 - - + -
87D PHE* 4.2 13.2 - - + -
92D LEU* 4.4 11.2 - - + +
118D VAL* 4.7 10.1 - - + -
119D PRO 5.9 0.4 - - - +
120D LEU* 5.4 1.6 - - + -
149D LEU* 4.0 25.6 - - + -
153D TRP* 4.2 14.4 - - + -
155D GLY 3.0 17.6 + - - +
156D SER 4.1 1.8 - - - +
158D ALA* 1.3 80.4 - - - +
160D PHE* 1.3 60.7 + - - +
161D GLN 3.5 0.7 + - - -
162D SER* 3.7 13.2 + - - -
163D SER* 4.8 0.9 + - - -
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Residues in contact with PHE 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D ALA* 3.8 34.8 - - + -
115D TYR* 3.9 28.7 - + + -
117D SER* 4.2 3.4 - - - -
118D VAL* 4.0 28.7 - - + -
149D LEU* 4.3 5.2 - - + -
156D SER 2.9 19.3 + - - +
157D PRO* 3.6 2.5 - - + +
158D ALA 3.2 0.2 - - - -
159D ILE* 1.3 75.0 - - - +
161D GLN* 1.3 65.1 + - - +
162D SER 3.2 2.7 - - - -
163D SER* 3.0 26.5 + - - -
164D MET* 2.9 53.9 + - + -
167D ILE* 4.3 14.1 - - + -
182D GLN* 4.8 2.2 - - - +
209D LEU* 6.2 0.2 - - + -
212D TRP* 4.3 8.3 - + - -
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Residues in contact with GLN 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D LEU* 2.6 31.6 + - + +
93D GLY 4.6 1.0 + - - -
94D ILE* 3.2 42.2 + - + +
95D PRO* 4.0 8.7 - - - +
157D PRO 2.9 10.9 + - - +
158D ALA* 3.2 14.3 + - - +
160D PHE* 1.3 76.1 - - - +
162D SER* 1.3 64.0 + - - +
164D MET* 3.0 8.2 + - + +
165D THR* 2.8 42.2 + - + +
182D GLN* 4.4 7.6 - - - +
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Residues in contact with SER 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D LEU* 5.8 5.0 - - - +
158D ALA 4.7 0.4 + - - -
159D ILE 3.7 12.2 + - - -
161D GLN* 1.3 76.3 - - - +
163D SER* 1.3 74.7 + - - -
165D THR* 2.8 22.7 + - - -
166D LYS* 3.2 28.1 + - - +
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Residues in contact with SER 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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118D VAL* 5.1 4.7 - - - +
159D ILE 4.8 0.7 + - - -
160D PHE* 3.0 36.0 + - - -
162D SER* 1.3 83.1 + - - +
164D MET* 1.3 57.4 + - - +
166D LYS* 3.4 11.5 + - - +
167D ILE* 3.0 38.4 + - - +
212D TRP* 5.6 4.3 - - - -
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Residues in contact with MET 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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111D VAL* 5.3 7.4 - - + -
114D ALA* 6.2 0.9 - - - -
115D TYR* 6.2 0.2 - - - -
160D PHE* 2.9 36.4 + - + +
161D GLN* 3.0 14.1 + - + +
163D SER* 1.3 74.9 - - - +
165D THR* 1.3 67.8 + - + +
167D ILE* 3.2 4.9 + - + +
168D LEU* 3.0 54.4 + - + +
182D GLN* 3.9 20.4 - - + +
187D LEU* 3.6 39.9 - - + -
209D LEU* 4.1 21.5 - - + -
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Residues in contact with THR 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D GLN* 2.8 33.7 + - + +
162D SER* 2.8 23.9 + - - -
164D MET* 1.3 73.2 - - + +
166D LYS* 1.3 57.5 + - - +
168D LEU* 3.3 7.1 + - + +
169D GLU* 2.8 35.8 + - - +
172D LYS* 5.4 11.7 - - - +
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Residues in contact with LYS 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D SER* 3.2 25.3 + - - +
163D SER* 3.7 10.4 - - - +
165D THR* 1.3 84.0 + - - +
167D ILE* 1.3 63.5 + - + +
169D GLU* 3.5 17.2 - - - +
170D PRO* 3.8 4.3 - - - +
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Residues in contact with ILE 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D PHE* 4.3 16.8 - - + -
163D SER* 3.0 20.7 + - - +
164D MET* 3.2 6.3 + - - +
166D LYS* 1.3 76.8 - - + +
168D LEU* 1.3 59.8 + - + +
170D PRO* 3.3 3.6 - - - +
208D HIS* 2.6 45.6 + - + -
209D LEU* 3.8 30.5 - - + -
212D TRP* 3.5 61.2 - - + +
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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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164D MET* 3.0 54.8 + - + +
165D THR* 4.1 4.7 - - + +
167D ILE* 1.3 77.9 - - + +
169D GLU* 1.3 66.2 + - - +
170D PRO* 3.2 1.8 - - - -
171D PHE* 3.2 5.5 + - - +
172D LYS* 2.9 47.3 + - + +
180D ILE* 3.8 28.5 - - + -
187D LEU* 4.2 6.1 - - + -
205D LEU* 3.6 30.1 - - + -
208D HIS* 4.6 3.4 - - + -
209D LEU* 5.1 5.8 - - + -
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Residues in contact with GLU 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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165D THR* 2.8 21.0 + - - +
166D LYS* 3.5 11.7 - - - +
168D LEU* 1.3 75.0 - - - +
170D PRO* 1.4 71.9 - - + +
172D LYS* 3.5 9.8 + - - +
173D LYS* 3.0 51.5 + - + +
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Residues in contact with PRO 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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166D LYS 3.8 5.6 - - - +
167D ILE 3.3 15.9 - - - +
168D LEU 3.4 0.7 - - - -
169D GLU* 1.4 92.3 - - + +
171D PHE* 1.3 62.5 + - - +
173D LYS* 3.1 8.5 + - + +
174D GLN* 2.9 36.9 + - + +
208D HIS* 3.4 20.2 - - + +
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Residues in contact with PHE 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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168D LEU 3.2 7.8 + - - +
170D PRO* 1.3 80.3 - - - +
172D LYS* 1.3 60.4 + - - +
174D GLN* 3.4 7.6 + - + +
175D ASN* 2.9 56.2 + - + -
178D ILE* 4.0 26.9 - - + -
180D ILE* 4.2 17.5 - - + -
189D VAL* 5.0 2.7 - - + -
201D LYS 3.7 26.5 - - - -
204D GLU* 3.9 14.4 - - + -
205D LEU* 3.3 49.1 - - + -
208D HIS* 4.0 16.6 - - + +
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Residues in contact with LYS 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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165D THR* 5.4 12.2 - - - +
168D LEU* 2.9 50.1 + - + +
169D GLU* 3.8 15.3 - - - +
171D PHE* 1.3 77.8 - - - +
173D LYS* 1.3 68.1 + - + +
175D ASN 3.0 6.4 - - - -
176D PRO* 3.0 29.6 - - + +
178D ILE 5.5 5.8 - - - +
180D ILE* 4.4 33.5 + - + +
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Residues in contact with LYS 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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169D GLU* 3.0 35.2 + - + +
170D PRO* 3.1 9.6 + - + +
172D LYS* 1.3 83.5 - - + +
174D GLN* 1.3 63.2 + - + +
176D PRO* 3.6 15.1 - - + +
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Residues in contact with GLN 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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170D PRO* 2.9 28.3 + - + +
171D PHE* 3.7 8.2 - - - +
173D LYS* 1.3 77.3 - - + +
175D ASN* 1.3 70.0 + - - +
176D PRO* 3.3 9.2 - - - +
204D GLU* 5.1 6.9 - - - +
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Residues in contact with ASN 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 PHE* 2.9 53.8 + - + +
172D LYS* 3.0 9.7 - - - +
174D GLN* 1.3 83.6 - - - +
176D PRO* 1.3 63.2 - - - +
177D ASP* 3.1 7.2 + - + +
178D ILE* 3.3 35.3 + - + +
201D LYS* 2.7 32.4 + - - +
204D GLU* 4.2 2.6 + - - -
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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