Contacts of the helix formed by residues 200 - 220 (chain A) in PDB entry 1VHQ
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 200 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A TYR* 3.6 10.4 + - - -
198A ALA* 3.4 6.2 + - - +
199A GLN* 1.4 87.6 + - - +
201A ILE* 1.3 64.9 + - + +
202A ALA* 3.2 10.8 + - - +
203A GLU* 3.0 41.2 + - - +
204A ALA 3.1 17.3 + - - -
33B SER* 3.8 12.8 - - - +
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Residues in contact with ILE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A HIS* 3.6 34.5 - - + +
27A LEU* 3.9 16.6 - - + -
195A TYR* 3.2 15.2 + - - +
200A ASN* 1.3 73.3 - - - +
202A ALA* 1.3 63.3 + - - +
204A ALA* 3.2 1.6 + - - +
205A ALA* 2.9 27.4 + - - +
26B VAL* 3.8 33.0 - - + +
29B LEU* 3.6 18.8 - - + +
30B LEU* 3.9 14.4 - - + +
33B SER* 3.4 22.9 - - - -
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Residues in contact with ALA 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ASN* 3.2 6.5 + - - +
201A ILE* 1.3 80.0 - - - +
203A GLU* 1.3 61.7 + - + +
205A ALA* 3.4 2.6 + - - +
206A SER* 3.1 22.0 + - - -
30B LEU* 4.3 11.2 - - - -
33B SER* 3.2 26.5 + - - +
34B ARG* 4.2 22.2 - - + +
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Residues in contact with GLU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A VAL* 3.7 34.2 - - + +
197A LEU 4.2 0.9 - - - +
198A ALA* 3.7 5.4 - - + -
199A GLN* 3.0 38.2 + - - +
200A ASN* 3.0 32.2 + - - +
202A ALA* 1.3 72.1 - - + +
204A ALA* 1.3 67.5 + - - +
206A SER* 2.7 25.6 + - - -
207A GLY 3.4 3.5 + - - -
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Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 4.2 11.0 - - + -
178A VAL* 4.6 3.1 - - - -
194A ALA* 4.8 6.8 - - - +
195A TYR* 3.7 33.0 - - + -
198A ALA* 3.7 14.7 - - + +
200A ASN 3.1 5.2 + - - +
201A ILE 3.2 7.2 + - - +
203A GLU* 1.3 81.0 - - - +
205A ALA* 1.3 62.6 + - - +
207A GLY* 3.3 1.4 + - - -
208A ILE* 3.0 32.3 + - + +
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Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.7 29.1 - - + +
201A ILE 2.9 17.7 + - - +
202A ALA* 3.7 4.7 - - - +
204A ALA* 1.3 76.2 - - - +
206A SER* 1.3 58.9 + - - +
208A ILE* 4.4 3.1 - - - -
209A ASP* 2.8 46.2 + - - +
30B LEU* 3.9 13.7 - - + -
34B ARG* 6.3 0.7 - - + -
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Residues in contact with SER 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A VAL* 4.6 0.5 - - - +
179A ASP* 3.7 24.4 - - - +
202A ALA 3.1 13.3 + - - -
203A GLU* 2.7 22.5 + - - +
205A ALA* 1.3 80.0 - - - +
207A GLY* 1.4 61.0 + - - +
209A ASP* 4.0 5.0 - - - +
210A LYS* 3.3 27.4 + - - +
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Residues in contact with GLY 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A VAL 3.2 21.1 + - - -
179A ASP* 4.3 7.4 - - - -
180A ASP 4.7 0.2 - - - -
181A ILE* 3.9 0.3 - - - +
192A THR* 3.9 16.8 + - - -
194A ALA* 6.0 1.6 - - - -
203A GLU 3.4 2.6 + - - -
204A ALA 3.3 5.1 + - - -
206A SER* 1.4 80.0 + - - +
208A ILE* 1.3 66.3 + - - +
210A LYS* 3.2 6.7 + - - +
211A LEU* 3.0 22.0 + - - +
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Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLU* 3.8 30.3 - - + +
27A LEU* 4.1 18.8 - - + +
28A THR* 3.7 33.9 - - - +
137A MSE 3.8 30.1 - - + -
192A THR* 4.7 2.5 - - + -
194A ALA* 4.3 12.1 - - + -
204A ALA* 3.0 21.2 + - + +
205A ALA* 4.0 4.7 - - - +
207A GLY* 1.3 74.1 - - - +
209A ASP* 1.3 67.5 + - - +
211A LEU* 3.2 7.1 + - - +
212A VAL* 2.9 28.8 + - + +
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Residues in contact with ASP 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 4.6 5.5 - - - +
31A ALA* 3.4 17.4 - - - +
34A ARG* 2.9 35.4 + - - +
205A ALA* 2.8 34.1 + - - +
206A SER* 4.0 5.3 - - - +
208A ILE* 1.3 72.6 - - - +
210A LYS* 1.3 59.4 + - + +
212A VAL* 4.0 1.0 - - - +
213A SER* 2.9 30.3 + - - -
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Residues in contact with LYS 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASP* 2.5 36.0 + - - +
180A ASP* 4.4 18.3 + - - +
181A ILE* 3.7 16.8 - - + +
206A SER* 3.3 14.5 + - - +
207A GLY* 3.2 8.9 + - - +
208A ILE 3.2 0.4 - - - -
209A ASP* 1.3 76.0 - - + +
211A LEU* 1.4 64.0 + - - +
213A SER* 3.5 5.0 + - - -
214A ARG* 3.0 24.9 + - - +
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 4.1 22.4 - - + -
135A GLY* 4.2 2.2 - - - -
136A PHE 3.7 25.6 - - - +
137A MSE 4.2 17.9 - - + -
181A ILE* 3.6 10.2 - - + +
190A VAL* 3.7 29.6 - - + +
191A THR 4.1 0.7 - - - -
192A THR* 3.7 28.3 - - + +
207A GLY 3.0 13.6 + - - +
208A ILE* 3.2 6.5 + - - +
210A LYS* 1.4 77.6 - - - +
212A VAL* 1.3 66.3 + - + +
214A ARG* 3.3 2.3 + - - +
215A VAL* 2.9 40.0 + - + +
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 4.4 11.7 - - + +
31A ALA* 3.9 30.5 - - + +
32A ILE* 4.0 20.4 - - + +
35A SER* 4.9 1.3 - - - +
93A ILE* 4.0 20.0 - - + -
208A ILE* 2.9 29.0 + - + +
209A ASP 4.1 0.9 - - - +
211A LEU* 1.3 77.9 - - + +
213A SER* 1.3 68.4 - - - +
215A VAL* 3.2 5.7 + - - +
216A LEU* 2.9 40.7 + - + +
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Residues in contact with SER 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A SER* 5.8 2.2 - - - -
209A ASP 2.9 19.2 + - - -
210A LYS* 3.8 6.1 - - - -
212A VAL* 1.3 79.7 - - - +
214A ARG* 1.3 56.7 + - - +
216A LEU* 3.3 8.9 + - - +
217A VAL* 3.0 36.4 + - - +
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Residues in contact with ARG 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ILE* 3.7 23.3 - - + -
183A VAL* 4.0 18.2 - - + +
185A GLU* 3.0 30.7 + - - -
190A VAL* 4.1 9.9 - - + -
210A LYS 3.0 18.8 + - - +
211A LEU 3.9 2.5 - - - +
213A SER* 1.3 76.2 - - - +
215A VAL* 1.4 63.5 + - - +
217A VAL* 3.3 29.7 + - - +
218A LEU* 2.9 53.4 + - + +
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Residues in contact with VAL 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 5.2 3.1 - - + -
91A ALA* 3.5 28.9 - - + -
92A LEU 5.1 0.4 - - - +
93A ILE* 4.2 19.1 - - + -
133A PRO* 3.5 15.9 - - + +
134A LEU 4.4 1.8 - - - +
135A GLY* 4.2 12.3 - - - +
190A VAL* 3.8 24.5 - - + -
211A LEU* 2.9 32.8 + - + +
212A VAL 3.6 5.8 - - - +
214A ARG* 1.4 76.4 - - - +
216A LEU* 1.3 58.9 + - + +
218A LEU* 3.3 4.6 + - - -
219A ALA* 2.8 25.1 + - - +
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Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS* 4.9 9.5 - - + +
7A ILE* 3.5 36.8 - - + -
32A ILE* 5.1 1.1 - - + +
35A SER* 3.3 37.5 - - - +
37A ALA* 4.1 16.2 - - + -
93A ILE* 6.5 0.2 - - + -
212A VAL* 2.9 33.9 + - + +
213A SER* 3.6 6.5 - - - +
215A VAL* 1.3 73.5 - - + +
217A VAL* 1.3 62.3 + - + +
219A ALA* 3.1 4.4 + - + +
220A GLU* 2.8 30.1 + - - +
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A SER* 3.0 26.7 + - - +
214A ARG* 3.6 30.1 - - - +
216A LEU* 1.3 75.3 - - + +
218A LEU* 1.3 64.6 + - + +
220A GLU* 3.0 30.1 + - + +
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Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PRO* 3.8 24.2 - - + +
183A VAL* 4.5 6.3 - - + -
185A GLU* 4.7 5.8 - - - +
188A LYS* 4.4 38.0 + - + +
190A VAL* 3.9 25.6 - - + -
214A ARG* 2.9 56.9 + - + +
215A VAL 3.7 4.0 - - - +
217A VAL* 1.3 77.5 - - + +
219A ALA* 1.3 58.8 + - - +
220A GLU 4.4 2.4 - - - -
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Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS* 2.9 25.4 + - + +
7A ILE* 5.3 1.1 - - + -
90A ASP* 3.7 33.7 - - + +
91A ALA* 4.4 4.3 - - + -
133A PRO* 3.8 10.1 - - + +
215A VAL 2.8 17.1 + - - +
216A LEU* 3.1 8.0 + - - +
218A LEU* 1.3 74.2 - - - +
220A GLU* 1.3 65.0 + - - +
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Residues in contact with GLU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS* 3.5 20.3 + - + +
216A LEU 2.8 12.8 + - - +
217A VAL* 3.0 24.0 + - + +
218A LEU 4.4 2.2 - - - -
219A ALA* 1.3 82.0 - - - +
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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
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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