Contacts of the helix formed by residues 16 - 36 (chain A) in PDB entry 2VDY
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 GLY 16 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 1.3 64.8 + - - -
18A ALA 3.5 2.7 - - - -
19A SER* 3.6 12.6 + - - -
20A ALA* 3.2 25.2 + - - +
73A PHE* 5.7 1.3 - - - -
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Residues in contact with LEU 17 (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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16A GLY* 1.3 70.0 - - - -
18A ALA* 1.3 58.9 + - - +
20A ALA* 3.3 3.7 + - - -
21A ASN* 2.8 59.9 + - - +
73A PHE* 3.7 23.1 - - + -
82A GLU 4.7 4.0 - - - +
83A ILE* 3.7 31.9 - - + +
86A GLY* 3.7 34.5 - - - +
87A PHE* 4.0 9.9 - - + +
90A LEU* 4.4 9.9 - - + -
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Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY 3.5 0.6 - - - -
17A LEU* 1.3 78.1 - - - +
19A SER* 1.3 60.6 + - - +
21A ASN* 4.2 5.1 - - - +
22A VAL* 3.4 24.9 + - - +
370A THR 3.8 22.7 - - - +
371A TRP* 4.1 27.5 - - + +
372A SER* 6.1 1.3 - - - +
1384A HCY 3.8 5.4 - - - +
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Residues in contact with SER 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY* 3.6 14.4 + - - -
17A LEU 3.3 0.2 - - - -
18A ALA* 1.3 75.8 - - - +
20A ALA* 1.3 64.4 + - - +
22A VAL* 3.4 5.8 - - - +
23A ASP* 3.3 27.7 + - - -
260A ARG* 3.3 27.1 + - - +
1384A HCY 3.4 17.8 + - - -
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Residues in contact with ALA 20 (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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16A GLY 3.2 16.5 + - - +
17A LEU 3.3 1.8 + - - +
19A SER* 1.3 76.9 - - - +
21A ASN* 1.3 64.2 + - - +
23A ASP* 3.5 7.0 + - - +
24A PHE* 3.1 23.4 + - - +
71A LEU 3.7 5.6 - - - +
72A GLY* 3.3 29.0 - - - +
73A PHE* 3.7 22.0 - - + -
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Residues in contact with ASN 21 (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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17A LEU* 2.8 37.5 + - - +
18A ALA* 4.2 5.3 - - - +
20A ALA* 1.3 74.4 - - - +
22A VAL* 1.3 57.9 + - - +
24A PHE* 3.5 6.5 + - - +
25A ALA* 3.0 25.1 + - - +
45A PRO* 5.3 1.4 - - - +
46A VAL* 5.3 4.9 - - - +
49A SER* 4.0 17.4 + - - +
71A LEU 5.0 1.1 - - - +
73A PHE* 3.6 24.3 - - - -
87A PHE* 3.6 29.4 - - - -
90A LEU* 4.2 9.3 - - - +
372A SER* 5.2 8.6 + - - +
373A SER* 5.4 2.4 - - - +
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Residues in contact with VAL 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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18A ALA 3.4 14.2 + - - +
19A SER 3.4 11.9 - - - +
21A ASN* 1.3 75.4 - - - +
23A ASP* 1.3 66.6 + - - +
25A ALA* 3.3 5.4 + - - +
26A PHE* 3.2 47.0 + - + -
260A ARG* 3.5 28.0 - - + -
366A PHE* 3.8 27.6 - - + -
371A TRP 4.6 4.0 - - - +
373A SER* 4.5 8.0 - - - +
1384A HCY 3.9 16.2 - - + -
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Residues in contact with ASP 23 (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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19A SER* 3.3 18.7 + - - +
20A ALA* 3.8 6.0 - - - +
22A VAL* 1.3 73.6 - - - +
24A PHE* 1.3 63.0 + - - +
26A PHE* 3.8 5.9 + - - +
27A SER* 3.3 24.8 + - - -
72A GLY* 6.4 0.9 - - - -
259A SER* 5.8 0.3 - - - -
260A ARG* 2.7 52.6 + - - +
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Residues in contact with PHE 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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20A ALA 3.1 16.5 + - - +
21A ASN* 3.6 5.4 - - - +
23A ASP* 1.3 75.2 - - - +
25A ALA* 1.3 63.9 + - - +
27A SER* 4.0 3.1 - - - -
28A LEU* 2.9 54.8 + - + +
45A PRO* 4.7 2.7 - - + -
48A ILE* 3.7 30.3 - - + -
49A SER* 3.3 24.7 - - - +
52A LEU* 4.3 5.6 - - + -
70A GLY 3.4 23.6 - - - +
71A LEU* 3.7 35.4 - - + +
72A GLY* 5.7 0.4 - - - -
294A LEU* 4.6 3.1 - - + -
297A MET* 3.6 22.4 - - + -
299A ILE* 4.6 7.2 - - + -
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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
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21A ASN 3.0 14.5 + - - +
22A VAL* 3.3 10.8 - - + +
24A PHE* 1.3 77.7 - - - +
26A PHE* 1.3 59.0 + - + +
28A LEU* 3.8 5.5 - - - +
29A TYR* 3.0 28.4 + - - +
45A PRO* 3.5 31.6 - - + -
373A SER* 3.8 22.0 - - - +
376A LEU* 3.5 8.8 - - + +
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Residues in contact with PHE 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 VAL* 3.2 41.9 + - + +
23A ASP* 4.3 6.7 - - - +
25A ALA* 1.3 75.4 - - + +
27A SER* 1.3 60.6 + - - +
29A TYR* 3.5 5.1 - - + +
30A LYS* 2.9 39.1 + - - +
258A LEU* 3.7 32.5 - - + +
259A SER* 3.6 35.2 - - - -
260A ARG 4.0 2.7 - - - -
263A ILE* 3.9 24.0 - - + -
364A MET* 4.0 20.9 - - - -
366A PHE* 4.0 9.0 - + - -
373A SER* 5.5 0.2 - - - -
376A LEU* 4.2 20.4 - - + -
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Residues in contact with SER 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 ASP 3.3 17.8 + - - -
24A PHE* 4.6 0.2 - - - -
26A PHE* 1.3 76.2 - - - +
28A LEU* 1.3 59.5 + - - +
30A LYS* 3.5 9.5 + - - +
31A HIS* 2.8 57.8 + - - -
297A MET* 3.5 17.6 - - - +
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Residues in contact with LEU 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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24A PHE* 2.9 42.5 + - + +
25A ALA 3.8 3.6 - - - +
27A SER* 1.3 73.8 - - - +
29A TYR* 1.3 65.3 + - - +
32A LEU* 3.1 29.4 + - + +
43A ILE* 3.8 21.1 - - + -
45A PRO* 4.6 7.9 - - + -
48A ILE* 3.5 36.8 - - + -
290A LEU* 4.9 12.6 - - + -
293A VAL* 3.8 24.7 - - + +
294A LEU* 5.1 5.8 - - + -
297A MET* 3.8 16.7 - - + +
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Residues in contact with TYR 29 (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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25A ALA 3.0 18.7 + - - +
26A PHE* 3.5 7.4 - - - +
28A LEU* 1.3 77.3 - - - +
30A LYS* 1.3 58.9 - - + +
32A LEU* 3.3 5.2 + - - +
33A VAL* 2.9 40.1 + - + +
41A ILE* 4.2 14.3 - - + +
43A ILE* 4.2 14.6 - - + -
255A ILE* 3.9 18.7 - - + +
258A LEU* 3.7 30.3 - - + -
362A ILE* 3.8 16.3 - - + +
376A LEU* 3.7 34.1 - - + -
377A ALA 3.0 35.3 + - - -
378A ARG* 3.2 20.5 - - + +
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Residues in contact with LYS 30 (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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26A PHE* 2.9 24.9 + - - +
27A SER* 3.8 8.2 - - - +
29A TYR* 1.3 78.4 - - + +
31A HIS* 1.3 65.2 + - + +
33A VAL* 3.4 8.3 + - - +
34A ALA* 3.1 23.6 + - - +
255A ILE* 3.2 39.0 - - + +
256A ALA* 3.4 23.4 + - - +
257A ALA 4.7 0.2 - - - -
258A LEU* 2.7 28.6 + - + -
259A SER* 5.0 3.0 - - - -
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Residues in contact with HIS 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 SER* 2.8 43.5 + - - +
28A LEU 4.0 3.1 - - - +
30A LYS* 1.3 80.0 - - + +
32A LEU* 1.3 58.2 + - - +
34A ALA* 3.5 7.7 + - + +
35A LEU* 3.1 33.3 + - + +
293A VAL* 4.0 15.9 - - + +
296A GLU* 3.6 35.2 + - + +
297A MET* 3.4 21.6 - - + +
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Residues in contact with LEU 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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28A LEU* 3.1 19.4 + - + +
29A TYR 3.7 3.6 - - - +
31A HIS* 1.3 74.9 - - - +
33A VAL* 1.3 64.5 + - - +
35A LEU* 3.2 9.7 + - + +
36A SER* 3.0 37.8 + - - +
39A LYS* 5.9 0.7 - - - +
41A ILE* 4.0 21.1 - - + -
43A ILE* 3.8 34.8 - - + -
288A TYR* 4.3 28.7 - - + -
289A ASP 5.3 1.6 - - - +
290A LEU* 4.7 7.4 - - + -
293A VAL* 3.7 24.3 - - + +
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Residues in contact with VAL 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 TYR* 2.9 48.5 + - + +
30A LYS* 3.4 7.8 + - - +
32A LEU* 1.3 76.1 - - - +
34A ALA* 1.3 62.3 + - - +
36A SER 3.3 17.8 - - - +
37A PRO* 3.4 8.7 - - + +
41A ILE* 3.6 22.0 - - + -
252A ASN* 4.2 11.7 - - - +
255A ILE* 4.0 25.4 - - + -
378A ARG* 3.7 19.5 - - - +
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Residues in contact with ALA 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 LYS 3.1 16.7 + - - +
31A HIS* 3.8 7.9 - - + +
32A LEU 3.3 0.2 - - - -
33A VAL* 1.3 78.6 - - + +
35A LEU* 1.3 61.6 + - + +
36A SER 3.5 0.2 - - - -
37A PRO* 4.0 12.1 - - - +
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Residues in contact with LEU 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 HIS* 3.1 24.0 + - + +
32A LEU* 3.2 7.2 + - + +
34A ALA* 1.3 79.7 - - + +
36A SER* 1.3 60.9 + - - +
37A PRO* 3.9 4.8 - - - +
292A ASP* 4.0 26.2 - - + +
293A VAL* 3.8 42.6 - - + +
296A GLU* 4.3 16.8 - - + +
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Residues in contact with SER 36 (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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32A LEU* 3.0 22.1 + - - +
33A VAL 3.3 5.5 - - - +
35A LEU* 1.3 78.9 - - - +
37A PRO* 1.3 62.2 - - - +
38A LYS 3.4 2.8 + - - -
39A LYS* 3.9 34.6 + - - +
41A ILE* 3.8 8.0 - - - +
288A TYR* 5.4 0.2 - - - -
378A ARG* 2.9 18.4 + - - -
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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
------------------------------------------------------------
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