Contacts of the helix formed by residues 16 - 36 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 1.3 65.7 + - - +
18B ALA 3.5 2.2 - - - -
19B SER* 4.0 15.0 - - - -
20B ALA* 3.5 22.0 + - - +
73B PHE* 4.9 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLY* 1.3 71.4 - - - +
18B ALA* 1.3 65.7 + - - +
20B ALA* 3.5 9.9 + - - +
21B ASN* 3.5 25.2 + - - +
73B PHE* 3.7 25.8 - - + -
82B GLU* 3.4 26.7 - - + +
83B ILE* 3.5 30.5 - - + +
86B GLY* 3.8 20.6 - - - -
87B PHE* 4.8 4.3 - - + -
90B LEU* 5.9 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLY* 3.5 0.6 - - - -
17B LEU* 1.3 79.0 - - - +
19B SER* 1.3 61.6 + - - +
20B ALA 3.4 0.5 + - - -
21B ASN* 3.5 5.3 + - - +
22B VAL* 3.1 29.0 + - - +
370B THR 3.5 24.9 - - - +
371B TRP* 3.9 26.0 - - + +
372B SER* 6.1 1.1 - - - +
1384B HCY 3.9 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLY* 3.8 18.0 + - - -
17B LEU 3.3 0.2 - - - -
18B ALA* 1.3 80.5 - - - +
20B ALA* 1.3 60.6 + - - +
23B ASP* 3.2 25.9 + - - +
260B ARG* 3.1 33.2 + - - +
1384B HCY 3.4 17.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLY 3.5 10.3 + - - +
17B LEU 3.5 1.5 + - - +
18B ALA 3.3 1.0 - - - -
19B SER* 1.3 79.4 - - - +
21B ASN* 1.3 63.3 + - - +
23B ASP* 3.5 7.5 + - - +
24B PHE 3.3 16.8 + - - -
71B LEU 3.4 10.9 - - - +
72B GLY* 3.4 29.5 - - - +
73B PHE* 3.6 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 3.5 21.4 + - - +
18B ALA* 3.5 4.8 + - - +
19B SER 3.5 0.2 - - - -
20B ALA* 1.3 75.3 - - - +
22B VAL* 1.3 61.0 + - + +
23B ASP 3.4 0.2 - - - -
24B PHE* 4.0 6.5 - - - +
25B ALA* 3.1 26.2 + - - +
45B PRO* 5.1 1.4 - - - +
46B VAL* 5.6 5.2 - - + +
49B SER* 4.1 18.1 + - - +
71B LEU* 4.5 2.9 - - - +
73B PHE* 3.4 23.5 - - - -
87B PHE* 3.5 31.2 - - - -
90B LEU* 4.5 13.5 - - - +
372B SER* 5.6 5.7 + - - -
373B SER* 4.8 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ALA 3.1 19.0 + - - +
19B SER 4.3 0.9 - - - +
20B ALA 3.3 0.4 - - - -
21B ASN* 1.3 77.7 - - + +
23B ASP* 1.3 59.1 + - - +
25B ALA* 3.2 7.6 + - + +
26B PHE* 3.1 57.0 + - + -
260B ARG* 3.8 21.8 - - + -
263B ILE* 5.4 0.7 - - + -
366B PHE* 4.6 10.3 - - + -
371B TRP 3.7 21.3 - - - +
372B SER* 5.4 0.4 - - - -
373B SER* 4.9 5.6 - - - +
1384B HCY 3.7 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B SER* 3.2 15.8 + - - +
20B ALA* 3.5 9.5 + - - +
21B ASN 3.4 0.4 - - - -
22B VAL* 1.3 77.4 - - - +
24B PHE* 1.3 59.7 + - - +
26B PHE* 3.8 6.2 + - - +
27B SER* 3.2 25.3 + - - -
72B GLY* 5.6 6.0 - - - +
259B SER* 5.7 0.7 - - - -
260B ARG* 3.1 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA 3.3 7.6 + - - +
21B ASN* 4.0 4.7 - - - +
23B ASP* 1.3 76.4 - - - +
25B ALA* 1.3 63.5 + - - +
27B SER* 3.9 3.5 - - - -
28B LEU* 2.9 49.3 + - + +
45B PRO 4.5 3.1 - - - -
48B ILE* 3.9 29.8 - - + -
49B SER* 3.2 26.2 - - - +
52B LEU* 4.4 0.4 - - + -
70B GLY 3.5 22.9 - - - -
71B LEU* 3.6 39.0 - - + +
72B GLY* 5.7 0.4 - - - -
294B LEU* 4.4 11.9 - - + -
297B MET* 3.7 22.4 - - + -
299B ILE* 4.4 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASN 3.1 19.1 + - - +
22B VAL* 3.2 7.4 + - + +
24B PHE* 1.3 78.8 - - - +
26B PHE* 1.3 59.5 + - + +
28B LEU* 3.9 3.1 - - - +
29B TYR* 3.0 28.9 + - - +
43B ILE* 4.5 1.9 - - - +
45B PRO* 3.5 31.9 - - + -
373B SER* 3.6 20.0 - - - +
376B LEU* 3.5 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL* 3.1 43.6 + - + +
23B ASP* 4.3 5.6 - - - +
25B ALA* 1.3 75.0 - - + +
27B SER* 1.3 56.2 + - - +
29B TYR* 3.2 3.4 + + - +
30B LYS* 2.8 47.6 + - - +
258B LEU* 3.9 33.4 - - + +
259B SER* 3.6 37.0 - - - -
260B ARG 4.3 0.7 - - - -
263B ILE* 3.7 27.1 - - + -
364B MET* 3.9 20.0 - - - -
366B PHE* 4.3 6.7 - + - -
373B SER* 5.7 0.4 - - - -
376B LEU* 4.4 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASP 3.2 18.2 + - - -
24B PHE* 3.9 0.9 - - - -
26B PHE* 1.3 78.0 - - - +
28B LEU* 1.3 54.4 + - - +
30B LYS* 3.5 9.7 + - - +
31B HIS* 2.7 52.8 + - - -
297B MET* 3.5 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 2.9 41.3 + - + +
25B ALA 3.9 2.0 - - - +
27B SER* 1.3 72.9 - - - +
29B TYR* 1.3 64.9 + - - +
31B HIS* 3.4 2.7 + - - +
32B LEU* 3.1 36.3 + - + +
43B ILE* 3.9 16.6 - - + -
45B PRO* 4.9 4.5 - - + -
48B ILE* 3.5 30.3 - - + -
290B LEU* 4.2 17.9 - - + -
293B VAL* 3.9 23.6 - - + -
294B LEU* 4.8 6.5 - - + -
297B MET* 3.6 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA 3.0 19.4 + - - +
26B PHE* 3.4 6.7 - - - +
28B LEU* 1.3 77.9 - - - +
30B LYS* 1.3 58.9 + - + +
32B LEU* 3.3 5.9 + - - +
33B VAL* 2.9 44.5 + - + +
41B ILE* 4.4 14.8 - - + -
43B ILE* 4.3 10.1 - - + +
255B ILE* 3.7 27.4 - - + +
258B LEU* 3.7 31.4 - - + -
362B ILE* 3.6 12.6 - - + +
376B LEU* 3.7 33.2 - - + -
377B ALA 3.2 33.7 + - - -
378B ARG* 3.3 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 2.8 31.0 + - - +
27B SER* 3.8 8.6 - - - +
29B TYR* 1.3 75.3 - - + +
31B HIS* 1.3 58.8 + - + +
33B VAL* 3.4 8.5 + - - +
34B ALA* 3.1 28.2 + - - +
255B ILE* 3.4 35.2 - - + +
256B ALA* 3.6 19.0 + - - +
258B LEU* 2.9 32.7 + - - -
259B SER* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B SER* 2.7 44.0 + - - +
28B LEU* 3.7 4.7 - - - +
29B TYR 3.3 0.4 - - - -
30B LYS* 1.3 77.9 - - + +
32B LEU* 1.3 61.7 - - - +
34B ALA* 3.5 7.8 + - + +
35B LEU* 3.4 28.5 + - - +
293B VAL* 3.8 16.6 - - + -
296B GLU* 4.0 44.3 + - + +
297B MET* 3.7 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.1 36.6 + - + +
29B TYR* 3.7 4.3 - - - +
31B HIS* 1.3 75.1 - - - +
33B VAL* 1.3 63.6 + - - +
35B LEU* 3.3 9.0 + - + +
36B SER* 3.2 27.9 + - - -
41B ILE* 3.9 14.8 - - + -
43B ILE* 3.7 32.8 - - + -
288B TYR* 4.0 24.2 - - + -
289B ASP 5.7 0.7 - - - +
290B LEU* 4.4 13.5 - - + -
293B VAL* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TYR* 2.9 39.4 + - + +
30B LYS* 3.6 7.4 - - - +
32B LEU* 1.3 77.2 - - - +
34B ALA* 1.3 62.0 + - - +
35B LEU 3.3 0.2 + - - -
36B SER 3.3 19.2 - - - +
37B PRO* 3.8 4.3 - - - +
41B ILE* 3.6 19.7 - - + -
252B ASN* 4.5 12.6 - - - +
255B ILE* 4.0 34.3 - - + -
378B ARG* 3.4 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LYS 3.1 16.4 + - - +
31B HIS* 3.8 8.7 - - + +
32B LEU 3.3 0.4 - - - -
33B VAL* 1.3 77.5 - - - +
35B LEU* 1.3 63.0 + - + +
36B SER 5.1 0.2 - - - -
37B PRO* 5.1 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B HIS 3.4 14.6 + - - +
32B LEU* 3.3 12.0 + - + +
33B VAL 3.2 0.8 - - - -
34B ALA* 1.3 82.4 - - + +
36B SER* 1.3 59.7 + - - +
37B PRO* 3.7 8.0 - - - +
292B ASP* 6.0 3.6 - - + -
293B VAL* 3.8 30.1 - - + +
296B GLU* 4.2 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU 3.2 14.6 + - - -
33B VAL 3.3 8.2 - - - +
35B LEU* 1.3 78.0 - - - +
37B PRO* 1.3 56.3 - - - +
38B LYS 3.4 2.2 - - - -
39B LYS* 4.1 26.4 - - - +
41B ILE* 3.4 16.5 - - - +
288B TYR* 5.4 3.6 - - - -
378B ARG* 2.6 28.8 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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