Contacts of the helix formed by residues 144 - 163 (chain D) in PDB entry 5VQ9
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 GLU 144 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D TYR* 4.0 7.9 + - - +
142D ASP 3.3 6.2 - - - +
143D VAL* 1.3 79.3 - - - +
145D VAL* 1.3 64.0 + - - +
146D LYS* 3.3 3.6 - - - +
147D SER* 3.5 26.4 + - - +
148D HIS* 3.3 18.5 + - + -
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Residues in contact with VAL 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D TYR* 4.1 27.2 - - + +
142D ASP 4.9 0.7 - - - +
143D VAL* 4.1 22.4 - - + +
144D GLU* 1.3 76.6 - - - +
146D LYS* 1.3 64.8 + - - +
147D SER 3.2 0.3 + - - -
148D HIS* 3.3 8.7 + - - +
149D LEU* 2.9 28.1 + - + +
188D LEU* 5.1 1.6 - - + -
317D GLN* 3.5 43.7 - - + +
318D TYR 4.7 4.7 - - - +
319D ILE* 3.5 18.4 - - + -
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Residues in contact with LYS 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D TRP* 2.8 72.1 + - + +
137D ASP* 4.1 6.5 + - - +
139D LEU* 2.8 28.6 + - + +
141D TYR* 3.8 24.0 - - + +
144D GLU* 3.3 1.0 - - - -
145D VAL* 1.3 76.9 - - - +
147D SER* 1.3 57.4 + - - +
149D LEU* 3.7 6.1 - - - +
150D LEU* 2.9 31.7 + - - +
188D LEU* 4.2 15.7 - - + -
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Residues in contact with SER 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D TRP* 5.5 2.0 - - - -
144D GLU* 3.6 32.9 + - - +
145D VAL 3.2 0.6 - - - -
146D LYS* 1.3 75.5 - - - +
148D HIS* 1.3 64.3 + - - +
150D LEU* 3.4 6.6 + - - +
151D ASP* 2.8 41.6 + - - +
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Residues in contact with HIS 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D VAL* 3.7 24.6 + - + +
144D GLU* 3.3 14.7 + - + +
145D VAL* 3.3 8.5 + - - +
147D SER* 1.3 78.9 - - - +
149D LEU* 1.3 52.0 + - - +
151D ASP* 2.7 14.6 + - + +
152D TYR* 2.6 69.6 + + + -
317D GLN* 4.9 6.3 + - - +
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Residues in contact with LEU 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D TRP* 6.0 0.2 - - + -
145D VAL* 2.9 18.4 + - + +
146D LYS* 3.7 6.1 - - - +
148D HIS* 1.3 75.1 - - - +
150D LEU* 1.3 62.8 + - - +
152D TYR* 3.4 4.9 + - + +
153D VAL* 2.9 30.4 + - + +
175D VAL* 4.3 11.0 - - + -
177D LEU* 4.0 16.8 - - + -
188D LEU* 3.9 32.3 - - + -
192D LEU* 3.9 21.5 - - + -
315D ILE* 4.1 22.2 - - + -
317D GLN* 4.0 35.4 + - + +
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Residues in contact with LEU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D TRP* 4.1 20.6 - - + -
146D LYS 2.9 21.5 + - - +
147D SER* 3.7 6.1 - - - +
149D LEU* 1.3 73.1 - - - +
151D ASP* 1.3 57.4 + - - +
153D VAL* 3.9 1.1 - - - +
154D MET* 2.7 45.3 + - + +
192D LEU* 3.8 12.4 - - + +
195D LYS* 4.3 21.5 - - + +
196D LEU* 3.6 35.4 - - + +
199D ARG* 4.4 24.2 - - + +
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Residues in contact with ASP 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D SER* 2.8 27.4 + - - +
148D HIS* 2.7 15.3 + - + +
150D LEU* 1.3 75.7 - - - +
152D TYR* 1.3 60.8 + - + +
154D MET* 3.6 7.3 - - - +
155D THR* 2.8 36.1 + - - +
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Residues in contact with TYR 152 (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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148D HIS* 2.6 52.8 + + + +
149D LEU* 3.7 9.9 - - + +
151D ASP* 1.3 75.9 - - + +
153D VAL* 1.3 57.3 + - - +
155D THR* 3.2 6.3 + - - -
156D THR* 2.9 30.5 + - - -
315D ILE* 3.4 34.5 - - + +
316D LYS 5.8 3.1 - - - -
317D GLN* 4.7 9.4 - - - -
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Residues in contact with VAL 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D LEU* 2.9 17.6 + - + +
150D LEU 4.1 1.6 - - - +
152D TYR* 1.3 72.2 - - + +
154D MET* 1.3 67.1 + - - +
156D THR* 3.4 6.1 + - - -
157D LEU* 3.1 33.1 + - + +
175D VAL* 3.6 29.4 - - + -
192D LEU* 4.1 14.1 - - + -
196D LEU* 3.6 32.1 - - + -
294D VAL* 4.6 17.5 - - + -
296D LEU* 6.0 0.4 - - + -
315D ILE* 3.9 10.8 - - + -
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Residues in contact with MET 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D LEU* 2.7 29.1 + - + +
151D ASP* 3.6 10.1 - - - +
153D VAL* 1.3 74.4 - - - +
155D THR* 1.3 60.2 + - - +
157D LEU* 3.5 6.0 + - - +
158D LEU* 3.2 19.2 + - - +
196D LEU* 4.2 12.2 - - - +
199D ARG* 4.2 23.1 - - + +
200D LEU* 3.5 46.4 - - + -
203D ARG* 4.9 2.4 + - - -
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Residues in contact with THR 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D ASP* 2.8 21.7 + - - +
152D TYR* 3.6 5.4 - - - -
154D MET* 1.3 74.8 - - - +
156D THR* 1.3 67.2 + - - +
158D LEU* 2.9 23.1 + - + +
159D PHE* 2.9 42.8 + - + -
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Residues in contact with THR 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D TYR 2.9 15.8 + - - -
153D VAL* 3.6 12.8 - - + -
155D THR* 1.3 75.0 - - - +
157D LEU* 1.3 62.5 + - + +
159D PHE* 3.1 8.7 + - - +
160D SER* 2.8 27.3 + - - -
171D TRP* 3.7 25.4 - - + +
172D ASN 3.0 29.5 + - - +
173D ARG* 4.6 6.1 - - + +
294D VAL* 6.2 2.0 - - + -
315D ILE* 3.6 17.1 - - - +
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Residues in contact with LEU 157 (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 VAL* 3.1 30.2 + - + +
154D MET* 3.7 4.9 - - - +
155D THR 3.2 0.2 - - - -
156D THR* 1.3 78.1 - - + +
158D LEU* 1.3 53.1 + - - +
160D SER* 3.4 7.7 + - - -
161D ASP* 2.7 36.6 + - - +
173D ARG* 6.1 2.0 - - + +
196D LEU* 4.4 5.8 - - + -
200D LEU* 3.5 27.4 - - + -
203D ARG* 3.5 21.9 + - - +
204D TYR* 4.9 2.2 - - + +
246D LEU* 3.9 25.8 - - + -
291D SER 4.5 12.8 - - - +
293D VAL 5.1 0.7 - - - +
294D VAL* 3.7 25.8 - - + -
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Residues in contact with LEU 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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154D MET 3.2 13.0 + - - +
155D THR* 2.9 15.5 + - + +
157D LEU* 1.3 77.7 - - - +
159D PHE* 1.3 72.5 + - + +
161D ASP* 3.4 5.6 + - + +
162D LYS* 3.1 44.1 + - + +
203D ARG* 4.2 11.8 - - - +
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Residues in contact with PHE 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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155D THR* 2.9 38.5 + - + +
156D THR* 3.6 6.1 - - - +
158D LEU* 1.3 89.8 - - + +
160D SER* 1.3 65.5 + - - +
162D LYS* 3.3 0.9 + - + -
163D ASN 3.0 4.0 + - - -
164D VAL* 2.8 63.4 + - + -
169D ILE* 3.6 30.5 - - + -
170D THR 5.4 1.1 - - - -
171D TRP* 3.9 29.3 - + + -
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Residues in contact with SER 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D THR* 2.8 20.6 + - - -
157D LEU* 3.5 11.7 - - - -
159D PHE* 1.3 71.9 - - - +
161D ASP* 1.3 63.7 + - - +
163D ASN* 3.1 14.7 + - - +
171D TRP* 3.4 30.2 - - - -
173D ARG* 3.3 21.3 + - - -
291D SER* 3.4 23.5 + - - -
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Residues in contact with ASP 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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157D LEU 2.7 20.4 + - - +
158D LEU* 3.7 8.4 - - + +
159D PHE 3.2 0.2 - - - -
160D SER* 1.3 75.4 + - - +
162D LYS* 1.3 66.3 + - + +
163D ASN* 3.4 2.1 + - - +
203D ARG* 3.3 41.9 + - - +
204D TYR* 4.6 6.2 + - - -
291D SER* 5.8 4.9 - - - -
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Residues in contact with LYS 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D LEU* 3.1 35.0 + - + +
159D PHE* 4.2 2.2 - - + +
160D SER 3.3 0.2 - - - -
161D ASP* 1.3 79.4 - - + +
163D ASN* 1.3 70.1 + - - +
164D VAL* 3.2 12.5 + - + +
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Residues in contact with ASN 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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159D PHE 3.0 5.0 + - - -
160D SER* 3.1 12.9 + - - +
161D ASP 3.2 1.9 - - - +
162D LYS* 1.3 79.5 - - - +
164D VAL* 1.3 66.5 + - - +
165D ASN* 3.3 5.5 + - - +
171D TRP* 5.5 3.0 - - - -
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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
------------------------------------------------------------
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