Contacts of the helix formed by residues 16 - 30 (chain B) in PDB entry 3V4R
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 ASP 16 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLN 3.4 0.4 + - - -
15B GLY* 1.4 72.8 - - - +
17B GLN* 1.3 62.8 + - - +
18B PRO* 3.5 2.0 - - - -
19B LYS* 3.7 11.6 + - + +
20B ALA* 3.2 23.7 + - - +
409B GLU 4.0 7.7 - - - +
410B GLN* 3.4 19.9 - - - +
411B ILE* 2.9 30.8 + - - +
412B ILE* 3.1 34.3 + - + +
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Residues in contact with GLN 17 (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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12B GLN 4.7 0.7 - - - +
13B PRO* 3.6 14.3 - - + +
14B GLN* 3.3 30.3 + - - +
16B ASP* 1.3 74.7 - - - +
18B PRO* 1.4 69.0 - - + +
20B ALA* 3.2 2.4 + - - +
21B ILE* 3.0 31.9 + - + +
43B THR 3.0 20.2 + - - +
44B GLY* 2.9 30.1 + - - -
47B PHE* 4.0 20.8 - - - +
48B THR* 3.8 6.1 + - - +
410B GLN* 3.7 19.7 - - + +
412B ILE 6.0 1.3 - - - +
414B PRO* 5.7 5.3 - - - +
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Residues in contact with PRO 18 (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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13B PRO* 3.4 27.4 - - + +
14B GLN 3.6 5.6 - - - +
15B GLY 3.5 16.4 - - - +
16B ASP 3.6 0.9 - - - -
17B GLN* 1.4 91.9 - - + +
19B LYS* 1.4 59.9 + - - +
21B ILE* 3.5 8.7 + - + +
22B GLU* 3.1 25.3 + - - +
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Residues in contact with LYS 19 (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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16B ASP* 3.7 14.0 + - + +
17B GLN 3.4 0.4 - - - -
18B PRO* 1.4 78.6 - - - +
20B ALA* 1.4 61.3 + - - +
22B GLU* 3.6 5.1 + - - +
23B LYS* 3.1 26.2 + - - +
409B GLU 6.2 0.2 - - - +
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP 3.2 19.1 + - - +
17B GLN 3.2 4.9 + - - +
19B LYS* 1.4 75.2 - - - +
21B ILE* 1.4 56.8 + - - +
23B LYS* 3.2 4.9 + - - +
24B LEU* 2.9 31.4 + - - +
37B LEU* 4.5 3.4 - - + -
48B THR* 4.1 8.5 - - + -
408B VAL* 3.8 22.7 - - + +
409B GLU 4.6 3.8 + - - +
410B GLN* 3.7 26.5 - - + +
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PRO* 3.9 16.8 - - + -
17B GLN* 3.0 28.5 + - + +
18B PRO* 4.1 4.5 - - + +
20B ALA* 1.4 72.9 - - - +
22B GLU* 1.4 57.3 + - - +
24B LEU* 3.2 5.4 + - - +
25B VAL* 2.9 51.4 + - + +
48B THR* 3.7 23.3 - - + +
51B ASN* 3.6 47.3 - - + +
52B LEU* 4.0 7.6 - - + +
55B GLU* 5.5 2.0 - - + -
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Residues in contact with GLU 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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18B PRO 3.1 17.6 + - - +
19B LYS* 3.8 6.1 - - - +
20B ALA 3.4 0.2 - - - -
21B ILE* 1.4 74.9 - - - +
23B LYS* 1.4 56.8 + - - +
25B VAL* 4.0 3.5 - - - +
26B LYS* 3.1 32.2 + - - +
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Residues in contact with LYS 23 (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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19B LYS 3.1 17.7 + - - +
20B ALA 3.7 3.4 - - - +
22B GLU* 1.4 75.1 - - - +
24B LEU* 1.4 57.1 + - - +
26B LYS* 3.8 6.1 + - - +
27B GLY* 3.2 23.2 + - - -
35B GLN* 3.9 2.1 - - - +
408B VAL* 4.2 23.3 - - + +
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Residues in contact with LEU 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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20B ALA 2.9 17.2 + - - +
21B ILE* 3.9 4.7 - - - +
23B LYS* 1.4 73.7 - - - +
25B VAL* 1.4 63.7 - - - +
28B ILE* 3.4 10.2 + - - +
35B GLN* 3.4 27.4 + - + +
37B LEU* 6.5 2.5 - - + -
48B THR* 6.2 2.0 - - + -
52B LEU* 3.8 26.2 - - + +
390B VAL* 5.8 6.7 - - + -
408B VAL* 4.9 10.0 - - + +
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Residues in contact with VAL 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 2.9 35.9 + - + +
22B GLU* 4.2 3.6 - - - +
24B LEU* 1.4 72.6 - - - +
26B LYS* 1.4 65.4 + - - +
27B GLY 3.2 0.2 - - - -
28B ILE* 3.3 4.7 + - - +
29B GLN* 3.0 44.7 + - - +
52B LEU* 3.9 18.8 - - + -
55B GLU* 3.8 30.1 - - + -
56B VAL* 3.8 17.3 - - + -
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Residues in contact with LYS 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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22B GLU 3.1 19.1 + - - +
23B LYS* 3.9 6.7 - - - +
25B VAL* 1.4 75.2 - - - +
27B GLY* 1.3 52.5 + - - +
29B GLN* 3.3 14.4 + - - +
30B GLU* 2.7 39.3 + - - +
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Residues in contact with GLY 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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23B LYS 3.2 13.1 + - - -
24B LEU 3.6 0.2 + - - -
25B VAL 3.2 0.6 - - - -
26B LYS* 1.3 75.7 - - - +
28B ILE* 1.4 54.7 + - - +
30B GLU* 3.3 6.8 + - - +
31B GLY 3.3 4.9 + - - -
32B LYS* 2.8 35.8 + - - +
35B GLN* 3.4 24.9 - - - -
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Residues in contact with ILE 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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24B LEU 3.4 7.5 + - - +
25B VAL 3.3 7.4 + - - +
27B GLY* 1.4 73.3 - - - +
29B GLN* 1.4 64.9 + - + +
31B GLY* 3.1 16.1 + - - -
32B LYS 4.0 4.9 - - - +
35B GLN* 3.5 15.9 - - - +
52B LEU* 3.7 29.4 - - + -
56B VAL* 3.8 24.2 - - + -
58B LYS* 4.5 9.4 - - - +
334B MET* 3.8 23.6 - - + -
388B ASN* 3.9 32.9 + - + +
390B VAL* 4.5 7.2 - - + -
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Residues in contact with GLN 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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25B VAL* 3.0 38.0 + - + +
26B LYS* 3.6 15.1 - - - +
28B ILE* 1.4 80.1 - - + +
30B GLU* 1.4 55.1 + - - +
31B GLY* 3.2 4.3 + - - -
55B GLU 5.5 3.0 + - - -
56B VAL* 5.9 0.9 - - + -
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Residues in contact with GLU 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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26B LYS* 2.7 21.7 + - + +
27B GLY* 3.3 6.5 + - - +
28B ILE 3.3 0.4 - - - -
29B GLN* 1.4 69.4 - - - +
31B GLY* 1.3 58.7 + - - +
32B LYS* 3.5 3.4 + - + +
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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