Contacts of the helix formed by residues 21 - 35 (chain Z) in PDB entry 1VQM
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 VAL 21 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18860 A 3.2 17.7 + - - +
18870 U 2.8 31.2 - - - +
168A PRO* 6.3 0.4 - - + -
19Z GLY 3.7 0.2 - - - -
20Z ARG* 1.3 79.0 - - + +
22Z SER* 1.3 70.6 + - - +
24Z ARG* 2.7 30.0 + - - +
25Z ARG* 2.9 40.2 + - + +
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Residues in contact with SER 22 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18470 A 4.2 15.4 + - - -
18480 G 4.6 6.9 - - - -
18850 A 4.6 6.5 + - - -
18860 A 5.0 4.2 - - - -
168A PRO* 3.9 24.5 - - - +
170A VAL* 4.5 7.8 - - - -
18Z TYR* 4.2 25.2 + - - +
19Z GLY 3.8 7.4 + - - -
20Z ARG 3.4 0.4 - - - -
21Z VAL* 1.3 82.3 - - - +
23Z ARG* 1.3 57.3 + - - +
24Z ARG 3.1 1.9 + - - -
25Z ARG 3.6 0.2 + - - -
26Z VAL* 2.9 29.4 + - - +
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Residues in contact with ARG 23 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17710 U 2.8 46.1 + - - +
17720 C 3.5 11.8 + - - +
17730 G 3.3 13.5 + - - -
10Z ARG* 6.0 0.2 - - - -
11Z SER* 2.6 56.8 + - - -
14Z PHE* 3.5 14.1 - - + -
15Z GLY 3.7 13.1 + - - -
16Z ALA* 4.9 2.7 - - - +
17Z ARG 3.3 17.5 + - - +
18Z TYR* 4.9 2.5 - - + -
19Z GLY* 2.8 60.8 + - - +
20Z ARG* 3.1 7.5 + - - +
22Z SER* 1.3 77.5 - - - +
24Z ARG* 1.3 56.6 + - - +
25Z ARG 3.7 0.2 - - - -
26Z VAL* 4.2 4.7 - - - -
27Z ALA* 4.0 4.3 - - - +
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Residues in contact with ARG 24 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Z ARG* 2.8 20.4 + - + +
21Z VAL* 2.7 29.6 + - - +
23Z ARG* 1.3 74.3 - - - +
25Z ARG* 1.3 65.0 + - + +
27Z ALA* 3.4 7.0 - - - +
28Z GLU* 3.2 40.8 + - + +
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Residues in contact with ARG 25 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18490 G 5.9 2.4 + - - -
166A ASP* 3.8 24.2 + - - +
168A PRO* 4.4 16.3 - - + +
21Z VAL* 2.9 35.2 + - + +
22Z SER 4.2 2.7 - - - +
24Z ARG* 1.3 76.1 - - + +
26Z VAL* 1.3 56.5 + - - +
27Z ALA 3.1 1.6 - - - -
28Z GLU* 3.2 10.7 + - - +
29Z ILE* 2.6 49.1 + - + +
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Residues in contact with VAL 26 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LYS* 3.6 23.6 - - + +
168A PRO* 4.4 7.2 - - + -
170A VAL* 3.7 25.1 - - + -
11Z SER* 3.6 13.2 - - - +
13Z ARG* 4.2 0.7 - - - +
14Z PHE* 3.7 24.7 - - + -
22Z SER 2.9 23.8 + - - +
25Z ARG* 1.3 76.6 - - - +
27Z ALA* 1.3 56.8 + - - +
29Z ILE* 4.5 0.7 - - - -
30Z GLU* 2.9 72.0 + - - +
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Residues in contact with ALA 27 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Z ARG* 4.0 36.0 - - + +
11Z SER* 3.6 14.9 + - - +
23Z ARG 4.0 5.8 - - - +
24Z ARG* 3.4 11.8 + - - +
25Z ARG 3.1 0.6 - - - -
26Z VAL* 1.3 78.8 - - - +
28Z GLU* 1.3 53.1 + - + +
30Z GLU* 3.5 1.3 - - - +
31Z SER* 2.6 40.2 + - - -
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Residues in contact with GLU 28 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Z ARG* 3.2 41.4 + - - +
25Z ARG* 3.2 11.0 + - - +
27Z ALA* 1.3 78.1 - - + +
29Z ILE* 1.3 57.9 + - + +
31Z SER* 2.9 7.5 + - - -
32Z GLU* 2.7 38.7 + - - +
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Residues in contact with ILE 29 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ASP* 3.7 15.7 - - + +
167A LYS* 3.3 46.2 - - + +
25Z ARG* 2.6 31.6 + - + +
26Z VAL* 4.1 2.2 - - - +
28Z GLU* 1.3 74.2 - - + +
30Z GLU* 1.3 57.6 + - - +
32Z GLU* 3.6 4.5 + - - +
33Z MET* 2.9 34.3 + - + +
69Z TYR* 3.6 38.1 - - + +
70Z LYS* 6.1 0.7 - - - +
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Residues in contact with GLU 30 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16510 C 3.7 14.6 + - - -
167A LYS* 2.8 33.0 + - - +
10Z ARG* 4.9 11.3 - - - -
13Z ARG* 3.5 24.7 + - - -
26Z VAL* 2.9 42.2 + - - +
27Z ALA* 4.0 1.8 - - - +
29Z ILE* 1.3 73.5 - - - +
31Z SER* 1.3 58.1 + - - +
33Z MET* 3.5 17.7 - - + -
34Z ASN* 2.7 45.4 + - - +
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Residues in contact with SER 31 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7980 G 5.6 1.6 + - - -
27Z ALA 2.6 25.4 + - - -
28Z GLU* 3.3 8.1 - - - -
30Z GLU* 1.3 71.1 - - - +
32Z GLU* 1.3 58.2 + - - +
33Z MET 3.0 4.9 + - - -
34Z ASN* 3.5 4.4 + - - +
35Z GLU* 2.9 30.1 + - - +
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Residues in contact with GLU 32 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Z GLU 2.7 18.0 + - - +
29Z ILE* 3.8 5.2 - - - +
31Z SER* 1.3 72.7 - - - +
33Z MET* 1.3 57.0 + - - +
34Z ASN 3.5 0.2 - - - -
35Z GLU* 3.5 24.6 - - - +
37Z HIS* 3.2 23.5 - - + -
69Z TYR 4.5 2.7 - - - +
70Z LYS* 2.6 53.5 + - + +
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Residues in contact with MET 33 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16510 C 4.9 6.7 - - - +
16520 C 5.5 0.2 - - - +
167A LYS* 4.1 4.7 - - - +
29Z ILE* 2.9 24.6 + - + +
30Z GLU* 3.3 38.6 - - + +
31Z SER 3.0 0.4 - - - -
32Z GLU* 1.3 80.6 - - - +
34Z ASN* 1.3 65.8 + - - +
37Z HIS* 3.0 17.7 + - - -
48Z ASP* 6.0 0.3 - - - -
49Z ARG* 4.1 33.2 + - + +
55Z TRP* 3.8 17.2 - - + -
69Z TYR* 2.9 51.4 - - + +
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Residues in contact with ASN 34 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7970 A 4.4 14.1 + - - -
7980 G 5.5 12.3 - - - -
16500 C 4.0 15.9 + - - -
30Z GLU* 2.7 31.1 + - - +
31Z SER* 3.5 3.9 + - - +
33Z MET* 1.3 83.3 - - - +
35Z GLU* 1.3 67.3 + - - +
36Z ASP* 3.8 2.6 + - - +
48Z ASP* 5.0 6.9 - - - +
49Z ARG* 6.2 0.3 - - - +
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Residues in contact with GLU 35 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Z SER* 2.9 22.2 + - - +
32Z GLU* 3.5 33.4 + - - +
33Z MET 3.4 1.6 - - - -
34Z ASN* 1.3 82.2 - - - +
36Z ASP* 1.3 65.7 + - - +
37Z HIS* 2.8 33.6 + - + +
47Z VAL 3.9 3.6 - - - +
48Z ASP* 5.3 0.3 - - - +
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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