Contacts of the helix formed by residues 14 - 29 (chain B) in PDB entry 3QVL
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 SER 14 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B ASN* 3.1 1.9 + - - -
12B ASN* 3.0 16.1 + - - -
13B THR* 1.3 75.1 + - - +
15B LEU* 1.3 54.4 + - - +
16B ALA* 3.6 8.7 + - - +
17B MET* 3.2 23.2 + - - +
18B THR* 2.7 34.8 + - - -
45B PRO* 3.6 16.4 + - - -
151B LEU* 3.9 18.0 - - - +
154B GLU* 4.5 1.4 - - - +
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Residues in contact with LEU 15 (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 THR 3.1 9.8 + - - +
14B SER* 1.3 71.8 - - - +
16B ALA* 1.3 62.7 + - - +
18B THR* 3.4 13.7 + - + -
19B GLU* 3.1 43.0 + - + +
39B CYS* 5.4 9.2 - - - -
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Residues in contact with ALA 16 (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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14B SER* 3.2 8.0 + - - +
15B LEU* 1.3 78.8 - - - +
17B MET* 1.3 57.3 + - - +
19B GLU* 3.4 14.3 + - - +
20B THR* 3.1 26.9 + - - -
154B GLU* 3.3 29.9 - - + +
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Residues in contact with MET 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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1B 5HY 4.2 11.4 - - - -
10B ASN* 3.8 11.2 - - - +
12B ASN* 3.3 24.5 - - - +
14B SER* 3.2 12.3 + - - +
16B ALA* 1.3 74.7 - - - +
18B THR* 1.3 60.9 + - - +
19B GLU 3.2 0.7 - - - -
20B THR* 3.2 0.9 + - - -
21B ILE* 2.8 43.4 + - + +
150B VAL* 3.6 30.7 - - + +
151B LEU* 4.0 15.0 - - + -
154B GLU* 3.5 33.1 - - + +
185B GLY 4.6 0.9 - - - -
186B GLY* 4.0 27.1 - - - -
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Residues in contact with THR 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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8B VAL 5.6 0.2 - - - +
10B ASN* 2.8 21.6 + - + +
14B SER 2.7 22.5 + - - -
15B LEU* 3.6 15.5 - - + -
16B ALA 3.4 0.2 - - - -
17B MET* 1.3 76.0 - - - +
19B GLU* 1.3 56.8 + - + +
21B ILE* 3.8 2.8 - - + +
22B GLY* 2.8 26.9 + - - -
37B ALA* 4.1 20.8 - - + +
38B VAL* 3.9 26.9 - - - +
39B CYS* 3.6 13.5 - - + +
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Residues in contact with GLU 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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15B LEU* 3.1 34.9 + - + +
16B ALA* 3.5 12.4 - - - +
18B THR* 1.3 75.4 - - + +
20B THR* 1.3 58.1 + - - +
22B GLY* 4.0 0.8 - - - -
23B ALA* 3.0 30.7 + - - +
26B ARG* 4.7 3.7 + - - +
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Residues in contact with THR 20 (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 ALA 3.1 10.2 + - - -
17B MET* 3.2 7.6 + - - -
19B GLU* 1.3 73.7 - - - +
21B ILE* 1.3 64.4 - - - +
23B ALA* 3.5 6.4 + - - +
24B ALA* 3.2 22.5 + - - +
154B GLU* 3.1 23.5 + - - +
185B GLY 4.4 9.6 - - - +
186B GLY 3.9 19.1 - - - +
188B ALA* 4.6 0.4 - - + -
189B THR* 3.8 31.1 - - + +
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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
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8B VAL* 3.5 31.4 - - + +
10B ASN* 3.7 29.2 - - + +
17B MET* 2.8 29.8 + - + +
18B THR* 3.9 5.2 - - + +
20B THR* 1.3 74.1 - - - +
22B GLY* 1.3 65.4 + - - +
24B ALA* 3.3 3.0 + - - -
25B ALA* 3.0 21.8 + - - +
37B ALA* 5.7 1.3 - - + -
78B ALA* 3.6 31.9 - - + +
185B GLY* 3.5 24.0 - - - +
188B ALA* 4.8 0.2 - - - -
206B VAL* 3.5 18.4 - - + +
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Residues in contact with GLY 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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8B VAL* 5.8 0.2 - - - -
18B THR 2.8 18.3 + - - -
19B GLU* 4.0 1.8 - - - -
21B ILE* 1.3 76.6 - - - +
23B ALA* 1.3 56.2 + - - +
25B ALA* 3.4 6.2 + - - +
26B ARG* 3.0 46.1 + - - +
35B ILE* 4.4 0.6 - - - +
37B ALA* 3.8 21.3 - - - -
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Residues in contact with ALA 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 GLU 3.0 19.8 + - - +
20B THR* 3.7 6.5 - - - +
21B ILE 3.3 0.2 - - - -
22B GLY* 1.3 75.4 - - - +
24B ALA* 1.3 61.0 + - - +
26B ARG* 3.5 18.8 + - - +
27B ALA* 3.1 25.3 + - - +
189B THR* 4.7 9.6 - - + -
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Residues in contact with ALA 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 THR 3.2 11.2 + - - +
21B ILE 3.3 3.6 + - - +
23B ALA* 1.3 76.9 - - - +
25B ALA* 1.3 62.4 + - - +
27B ALA* 3.6 12.5 + - - +
28B VAL* 3.7 16.3 + - - +
188B ALA* 3.6 38.4 - - + +
189B THR* 4.3 6.7 - - + +
204B ASP* 3.9 11.2 - - - +
206B VAL* 4.3 3.8 - - + -
207B SER* 4.1 5.9 - - - -
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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
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8B VAL* 4.0 7.6 - - + -
21B ILE 3.0 17.1 + - - +
22B GLY* 3.6 6.1 - - - +
23B ALA 3.3 0.2 - - - -
24B ALA* 1.3 78.5 - - - +
26B ARG* 1.3 60.7 + - - +
28B VAL* 3.6 6.2 + - - +
29B ALA* 3.2 22.9 + - - +
35B ILE* 3.8 22.2 - - + +
206B VAL* 4.1 7.1 - - + +
207B SER* 5.1 0.4 - - - +
210B VAL* 3.7 29.0 - - + +
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Residues in contact with ARG 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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19B GLU* 4.7 3.6 + - - +
22B GLY* 3.0 32.7 + - - +
23B ALA* 3.7 26.5 - - - +
25B ALA* 1.3 75.0 - - - +
27B ALA* 1.3 65.0 + - - +
28B VAL 3.3 0.9 + - - -
29B ALA* 3.5 15.5 + - - +
35B ILE* 3.7 32.2 + - + +
37B ALA* 4.8 8.9 - - - +
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Residues in contact with ALA 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 ALA 3.1 18.3 + - - +
24B ALA* 3.8 9.2 - - - +
25B ALA 3.3 0.6 - - - -
26B ARG* 1.3 77.3 - - - +
28B VAL* 1.3 63.4 + - + +
29B ALA 5.2 0.6 - - - +
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Residues in contact with VAL 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 ALA 3.7 6.5 - - - +
25B ALA 3.6 10.1 - - - +
27B ALA* 1.3 81.8 - - + +
29B ALA* 1.3 68.8 + - - +
30B ALA* 4.4 0.2 - - - -
207B SER* 3.6 48.0 - - - +
210B VAL* 4.5 4.5 - - + -
211B LYS* 3.0 33.7 + - + +
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Residues in contact with ALA 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 ALA 3.2 17.5 + - - +
26B ARG* 3.5 13.2 + - - +
27B ALA 5.2 0.3 - - - +
28B VAL* 1.3 79.1 - - - +
30B ALA* 1.3 65.1 + - - +
31B PRO* 3.9 1.9 - - - +
33B THR* 4.1 22.2 - - + +
35B ILE* 4.2 12.8 - - + -
210B VAL* 4.4 4.3 - - + -
214B GLU* 3.5 11.2 - - - +
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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