Contacts of the helix formed by residues 21 - 35 (chain B) 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 GLU 21 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ARG 5.4 1.0 - - - +
75A ARG* 3.0 49.5 + - - +
16B VAL* 3.7 16.1 + - + +
20B SER* 1.3 68.7 - - - +
22B ILE* 1.3 61.1 + - - +
23B HIS* 2.7 32.8 + - - +
24B GLU* 2.8 45.4 + - + +
25B ALA* 2.9 29.3 + - - +
95B PRO* 5.0 0.3 - - - +
96B GLY 3.0 8.6 + - - +
97B GLY* 3.6 13.1 - - - +
195B TYR* 3.9 5.8 - - + -
231B ACT 3.7 8.1 - - - +
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A CYS* 3.7 24.7 - - - -
22A ILE* 3.5 28.7 - - + -
26A VAL* 3.8 13.2 - - + -
72A ARG* 3.6 36.5 + - + +
73A ILE* 3.9 9.2 - - - +
14B CYS* 3.8 15.9 - - - -
15B GLY* 3.7 18.6 - - - +
16B VAL 4.6 1.2 - - - +
20B SER 3.1 1.9 + - - +
21B GLU* 1.3 76.1 + - - +
23B HIS* 1.3 65.8 + - + +
25B ALA* 3.4 0.5 + - - +
26B VAL* 3.1 23.6 + - + +
73B ILE* 4.2 10.8 - - + -
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Residues in contact with HIS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 4.2 18.4 - - + -
29A LEU* 3.9 15.8 - - + +
72A ARG 5.7 0.2 - - - -
73A ILE 2.8 28.3 + - - -
74A THR* 5.2 3.6 - - - -
75A ARG* 4.0 13.5 - - + -
21B GLU* 2.7 19.4 + - - +
22B ILE* 1.3 74.4 - - + +
24B GLU* 1.3 56.7 + - - +
26B VAL* 3.9 0.3 - - - +
27B LEU* 2.8 38.2 + - + +
195B TYR* 2.7 35.5 + - + -
201B ILE* 3.4 31.5 - - + +
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLU* 2.8 32.7 + - + +
23B HIS* 1.3 73.2 - - - +
25B ALA* 1.3 61.5 + - - +
27B LEU* 3.9 0.7 - - - +
28B THR* 2.8 30.8 + - - -
95B PRO* 4.4 4.5 - - + -
96B GLY* 2.9 29.5 + - - -
137B MSE 3.4 17.9 - - - +
138B CSO 2.8 21.1 + - - +
194B ALA* 3.4 11.4 - - + +
195B TYR* 3.0 33.1 + - + +
208B ILE* 3.8 19.7 - - + +
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 5.6 1.2 - - + +
11B LEU* 4.0 22.4 - - + -
20B SER* 4.6 1.3 - - - -
21B GLU 2.9 17.8 + - - +
22B ILE 3.9 3.1 - - - +
24B GLU* 1.3 77.0 - - - +
26B VAL* 1.3 56.9 + - - +
28B THR* 3.3 3.8 + - - -
29B LEU* 3.0 34.6 + - + +
73B ILE* 4.0 26.7 - - + -
95B PRO* 4.1 14.9 - - + +
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ILE* 3.8 28.9 - - + +
23A HIS* 4.2 19.3 - - + +
26A VAL* 3.5 33.0 - - + -
27A LEU* 4.8 6.7 - - + -
201A ILE* 3.8 19.2 - - + +
22B ILE* 3.1 18.6 + - + +
25B ALA* 1.3 74.8 - - - +
27B LEU* 1.3 59.3 + - + +
29B LEU* 3.2 10.1 + - - +
30B LEU* 2.8 27.0 + - - +
73B ILE* 4.5 8.1 - - + -
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 4.8 5.6 - - + -
27A LEU* 6.0 0.2 - - + -
30A LEU* 3.6 35.0 - - + -
23B HIS* 2.8 28.6 + - + +
24B GLU 3.9 2.9 - - - +
26B VAL* 1.3 77.9 - - + +
28B THR* 1.3 58.4 + - - +
30B LEU* 3.4 10.8 + - + +
31B ALA* 3.0 29.1 + - - +
201B ILE* 3.9 24.5 - - + +
204B ALA* 4.2 4.9 - - + -
205B ALA* 3.8 35.9 - - + +
208B ILE* 4.0 24.2 - - + +
209B ASP* 4.6 4.7 - - - +
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Residues in contact with THR 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 4.5 9.0 - - + -
24B GLU 2.8 22.1 + - - -
25B ALA* 3.5 6.7 - - - -
27B LEU* 1.3 76.1 - - - +
29B LEU* 1.3 63.3 + - - +
31B ALA* 3.4 2.8 + - - +
32B ILE* 3.0 45.2 + - + +
93B ILE* 3.8 30.5 - - + -
95B PRO* 4.1 6.8 - - + +
137B MSE 3.3 22.7 - - - +
208B ILE* 3.6 10.6 - - - +
212B VAL* 4.3 5.4 - - + -
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Residues in contact with LEU 29 (chain B).
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* 4.0 24.0 - - + +
201A ILE* 3.6 14.4 - - + +
9B VAL* 4.3 14.6 - - + -
11B LEU* 5.9 0.9 - - + -
25B ALA* 3.0 21.8 + - + +
26B VAL* 3.2 7.6 + - - +
28B THR* 1.3 75.3 - - - +
30B LEU* 1.3 64.1 + - - +
32B ILE* 3.4 5.2 + - - +
33B SER* 3.0 24.6 + - - -
39B ALA* 3.6 28.3 - - + -
41B CYS* 3.8 17.7 - - - -
73B ILE* 4.2 21.1 - - + +
74B THR* 4.7 8.3 - - + -
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 3.7 22.7 - - + -
30A LEU* 3.8 20.6 - - + -
34A ARG* 5.5 1.6 - - - +
201A ILE* 3.9 22.1 - - + +
202A ALA* 4.3 4.9 - - - -
205A ALA* 3.9 25.6 - - + -
26B VAL 2.8 16.9 + - - +
27B LEU* 3.6 11.0 - - + +
28B THR 3.3 0.2 - - - -
29B LEU* 1.3 78.2 - - - +
31B ALA* 1.3 57.3 - - - +
33B SER* 3.3 1.7 + - - -
34B ARG* 2.8 66.7 + - + +
209B ASP* 5.9 0.4 - - - +
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU 3.0 14.6 + - - +
28B THR 3.9 1.8 - - - +
29B LEU 3.4 0.2 - - - -
30B LEU* 1.3 78.0 - - - +
32B ILE* 1.3 60.8 + - - +
34B ARG* 3.5 14.2 + - - +
35B SER* 2.8 31.3 + - - +
209B ASP* 3.5 25.1 - - - +
212B VAL* 3.8 29.2 - - + -
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Residues in contact with ILE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ILE* 3.7 24.2 - - + -
9B VAL* 3.7 30.3 - - + -
28B THR* 3.0 28.6 + - + +
29B LEU* 3.7 5.2 - - - +
31B ALA* 1.3 75.0 - - - +
33B SER* 1.3 60.8 + - - +
35B SER* 3.3 9.8 + - - -
37B ALA* 3.1 49.4 + - + +
38B GLN 3.9 2.2 - - - +
39B ALA* 3.8 25.1 - - + +
93B ILE* 4.5 1.3 - - + -
212B VAL* 4.1 17.7 - - + -
216B LEU* 5.2 0.9 - - + -
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Residues in contact with SER 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ASN* 3.6 15.2 + - - +
201A ILE* 3.4 18.7 - - - +
202A ALA* 3.2 26.3 + - - +
29B LEU 3.0 17.7 + - - -
30B LEU 3.6 2.0 - - - -
32B ILE* 1.3 74.6 - - - +
34B ARG* 1.3 66.6 + - - +
36B GLY* 3.0 14.0 + - - -
37B ALA 4.0 8.7 - - - -
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Residues in contact with ARG 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 5.5 0.6 - - - +
34A ARG* 5.0 9.3 - - - +
202A ALA* 4.3 13.5 - - + -
205A ALA* 6.3 0.2 - - + -
30B LEU* 2.8 57.5 + - + +
31B ALA* 3.8 16.4 - - - +
33B SER* 1.3 74.0 - - - +
35B SER* 1.3 59.5 + - - +
36B GLY* 3.3 1.1 + - - -
209B ASP* 2.8 40.8 + - - +
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ALA* 2.8 18.6 + - - +
32B ILE 3.6 4.7 - - - -
33B SER 3.1 0.8 - - - -
34B ARG* 1.3 75.4 - - - +
36B GLY* 1.3 58.6 + - - +
37B ALA* 3.3 2.2 + - - +
212B VAL* 5.0 1.2 - - - +
213B SER* 5.9 1.0 - - - -
216B LEU* 3.4 31.3 - - - +
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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