Contacts of the helix formed by residues 152 - 167 (chain D) in PDB entry 2V32
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 ASN 152 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C ASN* 5.2 4.6 - - - +
155C GLU* 2.8 40.4 + - - +
158C ARG* 3.9 13.3 - - - +
176C ASP* 3.4 15.1 - - - +
178C GLN* 5.7 1.6 + - - -
143D ILE* 6.0 0.2 - - - +
145D TYR* 4.8 1.0 + - - -
151D ARG* 1.3 74.0 - - - +
153D PHE* 1.3 61.5 + - - +
154D SER* 3.1 24.1 + - - -
155D GLU* 3.1 29.1 + - + +
156D ILE* 3.5 10.3 + - - +
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Residues in contact with PHE 153 (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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175C ALA* 4.5 2.7 - - + -
176C ASP* 3.5 4.9 + - - +
33D VAL* 6.5 0.4 - - + -
35D PHE* 4.6 14.1 - + + -
48D GLU* 3.7 42.6 - - + -
51D ARG* 4.1 18.8 - - + +
52D VAL* 3.5 28.0 - - + -
55D LEU* 3.7 24.9 - - + -
59D PHE* 4.9 9.1 - + + -
151D ARG* 3.9 35.4 - - + -
152D ASN* 1.3 70.9 + - - +
154D SER* 1.3 63.6 + - - +
155D GLU 3.2 0.2 - - - -
156D ILE* 3.3 29.9 + - + +
157D LEU* 3.1 26.7 + - - +
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Residues in contact with SER 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ASP* 4.3 6.7 + - - -
51D ARG* 5.0 10.3 + - - +
55D LEU* 5.0 2.0 - - - +
152D ASN* 3.1 11.8 + - - -
153D PHE* 1.3 76.2 - - - +
155D GLU* 1.3 58.5 + - - +
157D LEU* 3.5 10.3 + - - +
158D ARG* 3.0 27.0 + - - +
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Residues in contact with GLU 155 (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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145C TYR* 2.8 29.0 + - - +
152C ASN* 2.9 31.2 + - - +
155C GLU* 4.6 13.2 - - + -
145D TYR* 5.9 0.7 - - - +
152D ASN* 3.1 31.3 + - + +
154D SER* 1.3 75.4 - - - +
156D ILE* 1.3 67.0 + - + +
158D ARG* 2.8 47.1 + - - +
159D VAL* 3.0 24.2 + - + +
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Residues in contact with ILE 156 (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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33D VAL* 4.6 6.3 - - + -
59D PHE* 4.2 13.5 - - + -
130D VAL* 4.0 34.3 - - + -
132D ILE* 4.3 14.1 - - + -
141D LEU* 6.5 0.4 - - + -
143D ILE* 5.0 8.7 - - + -
151D ARG* 4.8 5.4 - - + -
152D ASN 3.8 12.1 - - - +
153D PHE* 3.3 40.8 + - + +
155D GLU* 1.3 79.6 - - + +
157D LEU* 1.3 62.1 + - - +
159D VAL* 3.3 9.1 - - + +
160D ILE* 3.0 44.5 + - + +
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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
----------------------------------------------------------
55D LEU* 4.2 22.9 - - + -
58D ASP* 3.8 26.9 - - + +
59D PHE* 3.9 31.9 - - + -
62D ARG* 3.9 38.0 + - - +
153D PHE 3.1 19.0 + - - +
154D SER* 4.0 8.3 - - - +
155D GLU 3.3 0.2 - - - -
156D ILE* 1.3 75.7 - - - +
158D ARG* 1.3 62.7 + - - +
160D ILE* 3.3 5.6 + - + +
161D ASP* 3.1 28.6 + - - +
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Residues in contact with ARG 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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145C TYR* 4.0 1.0 - - - -
149C THR* 5.0 1.8 - - - +
150C GLY 3.2 25.9 + - - -
151C ARG 3.8 0.6 - - - -
152C ASN* 3.7 20.8 - - - +
154D SER 3.0 16.0 + - - +
155D GLU* 2.8 45.4 + - - +
157D LEU* 1.3 75.9 - - - +
159D VAL* 1.3 69.5 + - - +
161D ASP* 3.3 10.6 + - - +
162D SER* 3.0 23.8 + - - -
173D THR* 5.0 2.0 + - - -
174D PRO 4.6 0.2 + - - -
176D ASP* 4.0 4.1 - - - +
177D TRP* 2.9 62.3 + - + +
178D GLN* 3.4 28.5 - - - +
179D PRO* 4.6 3.8 - - + -
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Residues in contact with VAL 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C TYR* 3.6 34.1 - - + +
149C THR* 3.9 7.6 - - + -
132D ILE* 3.7 22.9 - - + -
141D LEU* 3.8 19.7 - - + -
155D GLU* 3.0 28.9 + - - +
156D ILE* 3.3 18.2 - - + +
158D ARG* 1.3 82.0 - - - +
160D ILE* 1.3 61.4 + - - +
162D SER* 3.3 6.1 + - - -
163D LEU* 2.8 32.4 + - - +
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Residues in contact with ILE 160 (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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31D TRP* 5.5 3.6 - - + -
33D VAL* 4.1 9.4 - - + -
59D PHE* 3.6 35.2 - - + -
62D ARG* 4.2 10.1 - - - -
64D VAL* 3.9 20.0 - - + -
132D ILE* 4.2 22.2 - - + -
156D ILE* 3.0 29.6 + - + +
157D LEU* 3.3 9.2 + - + +
159D VAL* 1.3 74.6 - - - +
161D ASP* 1.3 53.5 + - - +
163D LEU* 3.1 7.7 + - - +
164D GLN* 2.8 59.3 + - + +
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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
----------------------------------------------------------
62D ARG* 2.8 48.9 + - - +
157D LEU 3.1 14.0 + - - +
158D ARG* 3.4 8.5 - - - +
160D ILE* 1.3 76.2 - - - +
162D SER* 1.4 62.7 + - - +
164D GLN* 3.4 7.3 + - - +
165D LEU* 3.0 24.3 + - - +
177D TRP* 4.1 7.2 - - + -
179D PRO* 3.5 31.1 - - + +
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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
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148C THR 3.9 2.6 + - - -
149C THR* 2.7 29.9 + - - -
158D ARG* 3.0 15.1 + - - -
159D VAL* 3.6 7.2 - - - -
161D ASP* 1.4 77.2 - - - +
163D LEU* 1.3 63.2 + - - +
165D LEU* 3.7 1.0 - - - +
166D THR* 2.9 26.2 + - - +
173D THR* 3.0 30.3 + - - +
177D TRP* 3.5 17.5 - - - -
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Residues in contact with LEU 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C PRO* 3.6 23.8 - - + -
148C THR* 4.1 3.6 - - - +
149C THR* 3.5 18.6 - - - +
31D TRP* 3.8 17.9 - - + -
132D ILE* 3.7 40.4 - - + -
140D LYS* 4.1 21.5 - - + +
141D LEU* 4.3 8.7 - - + -
159D VAL 2.8 26.9 + - - +
160D ILE* 3.6 5.6 - - - +
162D SER* 1.3 71.5 - - - +
164D GLN* 1.3 62.3 + - - +
166D THR* 3.3 5.9 + - - -
167D ALA* 3.1 25.6 + - - +
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Residues in contact with GLN 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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31D TRP* 3.5 47.9 - - + +
62D ARG* 2.8 40.7 + - - +
64D VAL* 4.3 1.0 - - - +
160D ILE* 2.8 42.5 + - + +
161D ASP* 3.9 6.4 - - - +
163D LEU* 1.3 76.3 - - - +
165D LEU* 1.3 60.5 + - - +
167D ALA* 3.6 5.9 - - - +
168D GLN* 3.3 31.9 + - - +
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Residues in contact with LEU 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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161D ASP 3.0 17.1 + - - +
162D SER 3.7 3.6 - - - +
164D GLN* 1.3 75.0 - - - +
166D THR* 1.3 59.6 + - + +
167D ALA 3.1 0.4 - - - -
168D GLN* 2.9 9.6 + - + +
169D LYS* 2.9 37.8 + - + +
171D VAL* 4.1 11.0 - - + -
173D THR* 4.4 5.2 - - + -
177D TRP* 3.9 10.3 - - + -
183D CYS* 3.8 19.1 - - - -
218D GLN* 3.6 42.2 - - + +
219D PRO* 4.2 22.2 - - + +
220D LYS* 5.7 5.6 - - + -
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Residues in contact with THR 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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148C THR* 3.4 50.3 + - - +
162D SER* 2.9 22.4 + - - +
163D LEU* 3.3 8.8 + - - -
165D LEU* 1.3 77.4 - - + +
167D ALA* 1.3 58.7 + - - +
168D GLN 3.3 0.2 - - - -
169D LYS 3.3 18.4 - - - +
171D VAL* 3.5 24.0 - - + +
172D ALA* 4.0 1.1 - - - -
173D THR* 4.0 14.4 - - + -
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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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31D TRP* 4.7 12.8 - - + -
163D LEU 3.1 17.7 + - - +
164D GLN* 3.6 10.3 - - - +
165D LEU 3.1 0.2 - - - -
166D THR* 1.3 79.1 + - - +
168D GLN* 1.3 60.2 + - + +
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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
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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