Contacts of the helix formed by residues 21 - 35 (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 GLU 21 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.6 16.0 + - + +
20A SER* 1.3 69.8 - - - +
22A ILE* 1.3 61.8 + - - +
23A HIS* 2.8 30.5 + - - +
24A GLU* 2.9 42.8 + - + +
25A ALA* 2.9 28.9 + - - +
95A PRO* 5.0 0.3 - - - +
96A GLY 2.9 8.7 + - - +
97A GLY* 3.5 11.6 - - - +
138A CSO 4.2 0.4 - - - +
195A TYR* 3.9 5.8 - - + -
231A ACT 3.8 8.7 - - - +
72B ARG 5.4 1.0 - - - +
75B ARG* 2.9 50.1 + - - +
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Residues in contact with ILE 22 (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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14A CYS* 3.7 26.9 - - - -
15A GLY* 3.6 18.8 - - - +
16A VAL 4.5 1.4 - - - +
20A SER 3.1 2.0 + - - +
21A GLU* 1.3 73.0 + - - +
23A HIS* 1.3 70.4 + - + +
25A ALA* 4.0 4.4 - - - +
26A VAL* 3.0 24.1 + - + +
73A ILE* 4.2 7.2 - - + -
14B CYS* 3.8 9.2 - - - -
22B ILE* 3.5 28.7 - - + -
26B VAL* 3.8 12.1 - - + -
72B ARG* 3.7 41.3 + - + +
73B ILE* 4.0 10.3 - - + +
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Residues in contact with HIS 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 2.8 18.8 + - - +
22A ILE* 1.3 72.8 - - + +
24A GLU* 1.3 55.5 + - - +
26A VAL* 3.8 0.3 - - - +
27A LEU* 2.8 38.1 + - + +
195A TYR* 2.7 35.7 + - + -
201A ILE* 3.6 32.4 - - + +
26B VAL* 4.2 17.9 - - + -
29B LEU* 4.0 14.6 - - + +
73B ILE 2.8 27.9 + - - -
74B THR* 4.5 4.2 - - - -
75B ARG* 4.0 15.1 - - + -
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Residues in contact with GLU 24 (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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21A GLU* 2.9 31.1 + - + +
23A HIS* 1.3 71.9 - - - +
25A ALA* 1.3 60.4 + - - +
27A LEU* 3.5 1.4 + - - +
28A THR* 2.8 34.3 + - - -
95A PRO* 4.3 0.7 - - - -
96A GLY* 2.9 32.9 + - - +
137A MSE 3.4 16.1 - - - +
138A CSO 2.8 23.6 + - - +
194A ALA* 3.3 12.0 - - + +
195A TYR* 2.9 34.0 + - + +
208A ILE* 3.8 18.8 - - + +
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 5.5 0.9 - - + +
11A LEU* 3.9 27.4 - - + -
20A SER* 4.5 1.6 - - - -
21A GLU 2.9 18.1 + - - +
22A ILE 4.0 2.5 - - - +
23A HIS 3.3 0.2 - - - -
24A GLU* 1.3 76.3 - - - +
26A VAL* 1.3 57.5 + - - +
28A THR* 3.2 4.5 + - - -
29A LEU* 3.0 33.4 + - + +
73A ILE* 4.0 22.4 - - + -
95A PRO* 4.0 14.9 - - + +
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Residues in contact with VAL 26 (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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22A ILE* 3.0 19.6 + - + +
25A ALA* 1.3 72.2 - - - +
27A LEU* 1.3 62.1 + - + +
29A LEU* 3.2 8.9 + - - +
30A LEU* 2.8 26.9 + - - +
73A ILE* 4.6 7.9 - - + -
22B ILE* 3.8 28.7 - - + +
23B HIS* 4.2 18.8 - - + +
26B VAL* 3.5 31.4 - - + -
27B LEU* 4.8 7.0 - - + -
201B ILE* 3.8 19.3 - - + -
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Residues in contact with LEU 27 (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* 2.8 29.6 + - + +
24A GLU 3.9 3.4 - - - +
26A VAL* 1.3 76.3 - - + +
28A THR* 1.3 55.9 + - - +
30A LEU* 3.3 11.0 + - + +
31A ALA* 2.9 30.7 + - - +
201A ILE* 3.9 25.4 - - + +
204A ALA* 4.2 9.9 - - + -
205A ALA* 3.7 37.5 - - + +
208A ILE* 4.1 17.5 - - + +
209A ASP* 4.6 3.5 - - - +
26B VAL* 4.8 5.4 - - + -
27B LEU* 6.0 0.4 - - + -
30B LEU* 3.7 33.4 - - + -
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Residues in contact with THR 28 (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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9A VAL* 4.5 11.4 - - + -
24A GLU 2.8 23.9 + - - -
25A ALA* 3.4 7.0 - - - -
27A LEU* 1.3 77.5 - - - +
29A LEU* 1.3 63.5 + - - +
31A ALA* 3.3 1.9 + - - +
32A ILE* 3.0 45.0 + - + +
93A ILE* 3.8 28.3 - - + -
95A PRO* 4.2 4.8 - - + +
137A MSE 3.5 22.0 - - - +
208A ILE* 3.7 10.8 - - - +
212A VAL* 4.4 5.8 - - + +
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.4 13.9 - - + -
11A LEU* 6.0 0.7 - - + -
25A ALA* 3.0 19.0 + - + +
26A VAL* 3.5 9.0 - - - +
28A THR* 1.3 77.1 - - - +
30A LEU* 1.3 57.1 + - - +
32A ILE* 3.8 4.0 - - - +
33A SER* 2.9 32.2 + - - -
39A ALA* 3.5 29.6 - - + +
41A CYS* 3.9 16.4 - - - -
73A ILE* 4.2 20.4 - - + +
74A THR* 4.8 8.7 - - + -
23B HIS* 3.9 25.6 - - + +
201B ILE* 3.5 12.1 - - + +
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL 2.8 16.5 + - - +
27A LEU* 3.6 11.4 - - + +
28A THR 3.3 0.2 - - - -
29A LEU* 1.3 76.3 - - - +
31A ALA* 1.3 56.7 + - - +
33A SER* 3.8 0.3 - - - -
34A ARG* 2.8 70.6 + - + +
209A ASP* 6.0 0.2 - - - +
27B LEU* 3.6 24.0 - - + -
30B LEU* 3.8 22.2 - - + -
34B ARG* 5.5 0.7 - - - +
201B ILE* 3.8 16.5 - - + +
202B ALA* 4.3 9.6 - - - -
205B ALA* 4.0 23.1 - - + -
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Residues in contact with ALA 31 (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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27A LEU 2.9 14.1 + - - +
28A THR 3.9 1.6 - - - +
30A LEU* 1.3 77.8 - - - +
32A ILE* 1.3 59.4 + - - +
34A ARG* 3.8 12.7 - - - +
35A SER* 2.6 33.7 + - - +
208A ILE* 5.2 0.2 - - + -
209A ASP* 3.4 27.6 - - - +
212A VAL* 3.9 28.3 - - + -
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Residues in contact with ILE 32 (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* 3.9 23.1 - - + -
9A VAL* 3.6 30.3 - - + -
28A THR* 3.0 34.2 + - + +
29A LEU* 3.8 4.7 - - - +
31A ALA* 1.3 78.3 - - - +
33A SER* 1.3 63.1 + - - +
35A SER* 3.4 5.3 + - - -
36A GLY 3.6 0.2 + - - -
37A ALA* 3.1 52.4 + - + +
38A GLN 3.9 1.8 - - - -
39A ALA* 3.7 24.9 - - + +
93A ILE* 4.6 1.3 - - + -
212A VAL* 4.0 18.2 - - + -
216A LEU* 5.2 0.7 - - - -
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Residues in contact with SER 33 (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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29A LEU 2.9 18.8 + - - -
30A LEU 3.8 0.7 - - - -
32A ILE* 1.3 74.4 - - - +
34A ARG* 1.3 64.4 + - - +
36A GLY* 3.2 14.4 + - - -
37A ALA 3.9 9.8 - - - +
200B ASN* 3.8 14.5 + - - +
201B ILE* 3.4 18.4 - - - +
202B ALA* 3.3 26.1 + - - +
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Residues in contact with ARG 34 (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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30A LEU* 2.8 56.9 + - + +
31A ALA* 3.8 12.0 - - - +
33A SER* 1.3 73.2 - - - +
35A SER* 1.3 58.4 + - - +
36A GLY 3.2 3.9 + - - -
209A ASP* 2.9 40.4 + - - +
30B LEU* 5.5 1.2 - - - +
34B ARG* 5.0 10.3 - - - +
202B ALA* 4.0 17.0 - - + -
205B ALA* 5.9 2.0 - - + -
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Residues in contact with SER 35 (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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31A ALA* 2.6 25.2 + - - +
32A ILE 3.8 2.9 - - - -
33A SER 3.2 0.6 - - - -
34A ARG* 1.3 77.7 + - - +
36A GLY* 1.3 59.6 + - - +
37A ALA* 3.4 2.0 + - - +
212A VAL* 4.9 1.9 - - - +
213A SER* 5.8 2.4 - - - -
216A LEU* 3.3 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