Contacts of the helix formed by residues 18 - 29 (chain D) in PDB entry 1VI9
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 18 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D GLN* 3.8 16.4 - - - -
10D SER* 3.2 17.8 + - - -
17D ALA* 1.3 70.2 - - - +
19D ASN* 1.3 58.3 + - - -
21D ALA* 3.1 1.7 + - - -
22D ALA* 3.0 28.1 + - - +
83D TYR* 5.3 2.0 - - - -
224D ASP* 2.9 29.4 + - - +
300D BME 5.0 1.0 + - - -
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Residues in contact with ASN 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ALA* 3.1 33.8 + - - +
9D GLN* 3.1 39.4 + - - +
10D SER 2.7 16.8 + - - +
11D HIS* 5.0 2.9 - - + +
18D GLY* 1.3 71.9 - - - -
20D SER* 1.3 56.5 + - - +
22D ALA* 5.3 0.2 - - - +
23D GLU* 2.8 39.7 + - + +
26D MSE 5.9 0.2 - - - +
33D VAL* 4.8 2.9 - - - +
35D PRO* 3.8 13.1 - - + +
36D LEU 3.6 6.1 + - - +
37D ASN* 3.0 25.2 + - - +
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Residues in contact with SER 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ARG* 4.7 13.3 + - - +
35C PRO* 6.3 0.2 - - - -
10D SER 3.8 0.2 + - - -
11D HIS* 3.1 16.5 + - - -
12D VAL* 2.8 48.9 + - - -
15D GLY 3.9 6.1 - - - -
16D HIS* 2.8 24.3 + - - -
17D ALA 3.0 12.9 + - - -
19D ASN* 1.3 77.5 - - - +
21D ALA* 1.3 58.6 + - - +
23D GLU* 4.8 3.8 - - - +
24D PHE* 5.5 2.8 + - - +
268D VAL* 4.9 1.2 - - - +
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Residues in contact with ALA 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D HIS* 3.7 15.3 - - + -
17D ALA* 3.4 25.4 + - - +
18D GLY 3.1 5.8 + - - +
20D SER* 1.3 81.3 - - - +
22D ALA* 1.3 58.1 + - - +
23D GLU 3.7 0.7 - - - -
25D PRO* 3.1 26.2 - - - +
221D GLY* 4.1 13.2 - - - +
224D ASP* 4.5 1.8 - - + -
225D VAL* 3.8 21.5 - - + +
266D LEU* 4.8 2.2 - - + -
268D VAL* 3.8 6.8 - - + +
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Residues in contact with ALA 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLN* 4.0 13.9 - - - +
18D GLY 3.0 15.1 + - - +
19D ASN* 5.3 0.2 - - - +
21D ALA* 1.3 77.7 - - - +
23D GLU* 1.3 63.7 + - - +
24D PHE 3.5 0.2 - - - -
25D PRO* 3.5 5.0 - - - +
26D MSE 3.0 42.2 + - + +
224D ASP 3.5 25.1 - - - +
225D VAL* 4.4 5.8 - - - +
228D GLY* 4.7 0.9 - - - -
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Residues in contact with GLU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLU* 2.6 32.2 - - - +
24C PHE* 4.3 1.2 - - - -
27C ARG* 3.0 15.8 + - - -
19D ASN* 2.8 30.7 + - + +
20D SER* 5.4 1.0 - - - +
22D ALA* 1.3 72.8 - - - +
24D PHE* 1.3 77.6 + - - +
26D MSE 3.6 2.4 - - - +
27D ARG* 2.8 67.5 + - - +
33D VAL* 3.8 25.1 - - + +
35D PRO* 4.5 7.9 - - + -
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Residues in contact with PHE 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C GLU* 4.2 1.1 - - - -
24C PHE* 3.6 31.0 - + - -
27C ARG* 3.3 54.5 - - + +
28C ARG* 3.7 2.9 - - - -
19D ASN 4.8 0.2 + - - -
20D SER 5.5 2.2 + - - +
21D ALA 4.7 0.8 + - - -
23D GLU* 1.3 90.7 + - - +
25D PRO* 1.3 67.8 - - + +
27D ARG* 3.3 3.6 + - - +
28D ARG* 2.8 36.9 + - + +
268D VAL* 4.0 24.5 - - + -
269D VAL* 4.1 8.1 - - + -
272D GLN* 3.5 47.6 - - + -
275D ILE* 5.4 0.4 - - + -
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Residues in contact with PRO 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ALA 3.1 26.9 - - - +
22D ALA 3.5 7.0 - - - +
24D PHE* 1.3 98.7 - - + +
26D MSE 1.3 59.6 + - - +
28D ARG* 3.3 9.8 + - + +
29D LEU* 3.2 19.6 + - - +
225D VAL* 4.3 16.4 - - + -
229D LEU* 3.5 23.2 - - + +
268D VAL* 3.9 21.8 - - + -
275D ILE* 4.1 20.4 - - + +
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Residues in contact with MSE 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 3.4 44.2 - - + -
7D ALA* 5.0 7.0 - - + -
9D GLN* 5.3 1.3 - - - -
19D ASN* 5.9 0.2 - - - +
22D ALA* 3.0 34.8 + - + +
23D GLU* 3.6 1.1 - - - +
25D PRO* 1.3 76.3 - - - +
27D ARG* 1.3 61.3 + - - +
29D LEU* 3.3 13.0 + - - +
30D GLY 3.5 0.2 + - - -
31D ALA* 3.3 21.2 + - - +
33D VAL* 3.6 28.9 - - + -
80D LEU* 5.2 2.7 - - + -
225D VAL 5.6 0.2 - - - +
228D GLY* 3.6 43.3 - - - +
229D LEU* 3.9 8.7 - - + +
231D LEU* 4.9 2.5 - - + -
232D VAL* 3.9 7.6 - - + +
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Residues in contact with ARG 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLY 5.3 1.6 + - - -
16C HIS* 4.0 22.9 + - - -
20C SER* 5.0 9.3 + - - +
23C GLU* 2.9 18.6 + - - -
24C PHE* 3.4 33.3 - - + +
269C VAL* 3.6 20.9 - - + +
272C GLN* 2.9 13.0 + - - -
23D GLU* 2.8 57.0 + - - +
24D PHE 3.6 1.6 - - - +
26D MSE 1.3 77.1 - - - +
28D ARG* 1.3 57.1 + - - +
29D LEU 3.1 0.2 - - - -
30D GLY* 2.8 19.4 + - - -
31D ALA 3.4 17.7 - - - +
32D ASN* 5.6 0.2 + - - -
33D VAL* 2.8 38.0 + - + +
35D PRO* 4.0 13.3 - - - +
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Residues in contact with ARG 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C PHE* 4.0 1.9 - - - -
28C ARG* 3.4 29.2 - - - +
272C GLN* 3.3 27.4 + - - -
273C ASP* 4.3 3.4 + - - -
24D PHE* 2.8 28.2 + - + +
25D PRO* 3.3 11.6 + - + +
27D ARG* 1.3 71.8 - - - +
29D LEU* 1.3 62.1 + - - +
272D GLN* 3.0 53.7 + - + +
273D ASP* 2.8 28.1 + - - +
275D ILE* 4.8 5.8 - - + -
276D ALA* 3.6 17.2 - - + +
277D LYS* 3.5 17.8 - - - +
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Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D PRO 3.2 14.5 + - - +
26D MSE 3.6 9.4 - - - +
27D ARG 3.1 1.2 - - - -
28D ARG* 1.3 75.8 - - - +
30D GLY* 1.3 57.6 + - - +
31D ALA 3.6 0.7 - - - -
229D LEU* 3.7 29.2 - - + -
232D VAL* 4.1 14.4 - - + -
233D LYS* 4.1 17.9 - - + -
236D GLN* 3.1 19.8 + - - +
246D HIS* 3.8 23.8 - - + +
275D ILE* 3.6 28.7 - - + +
276D ALA* 3.7 16.6 - - - +
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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