Contacts of the helix formed by residues 18 - 29 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLN* 3.5 19.7 + - - -
10C SER* 3.9 11.2 - - - -
17C ALA* 1.3 72.0 - - - +
19C ASN* 1.3 58.0 + - - -
21C ALA* 3.1 2.9 + - - +
22C ALA* 3.0 27.5 + - - +
224C ASP* 2.8 29.7 + - - +
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Residues in contact with ASN 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ALA* 3.0 40.6 + - - +
9C GLN* 3.0 42.5 + - - +
10C SER 2.9 14.8 + - - +
11C HIS* 5.1 2.0 - - + +
18C GLY* 1.3 70.8 - - - -
20C SER* 1.3 56.1 + - - +
22C ALA* 4.4 3.4 - - - +
23C GLU* 2.9 37.7 + - + +
33C VAL* 5.5 0.3 - - - +
35C PRO* 3.9 9.5 - - + +
36C LEU 3.8 4.8 + - - +
37C ASN* 3.1 26.3 + - - +
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Residues in contact with SER 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C HIS* 3.1 20.1 + - - -
12C VAL* 2.9 45.7 + - - -
15C GLY 4.0 5.2 - - - -
16C HIS* 2.6 31.6 + - - -
17C ALA 3.0 12.9 + - - -
19C ASN* 1.3 75.6 - - - +
21C ALA* 1.3 52.7 + - - +
23C GLU* 4.8 5.6 - - - +
24C PHE* 5.4 2.9 + - - +
268C VAL* 4.9 1.4 - - - +
27D ARG* 5.0 10.1 + - - +
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Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C HIS* 4.0 12.3 - - + -
17C ALA* 3.4 25.2 + - - +
18C GLY 3.1 10.0 + - - +
20C SER* 1.3 79.4 - - - +
22C ALA* 1.3 58.7 + - - +
23C GLU 3.7 0.4 - - - -
25C PRO* 3.1 26.1 - - - +
221C GLY* 4.2 6.7 - - - +
224C ASP* 4.1 7.4 - - + -
225C VAL* 3.3 22.9 - - + +
266C LEU* 5.2 1.6 - - + -
268C VAL* 4.1 4.0 - - - +
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Residues in contact with ALA 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLN* 3.8 15.5 - - - +
18C GLY 3.0 15.4 + - - +
19C ASN* 4.4 1.3 - - - +
21C ALA* 1.3 77.9 - - - +
23C GLU* 1.3 64.8 + - - +
25C PRO* 3.1 5.0 - - - +
26C MSE 3.0 42.2 + - + +
80C LEU* 5.0 1.6 - - + -
224C ASP 3.7 22.2 - - - +
225C VAL* 4.6 4.3 - - - +
228C GLY* 4.8 2.2 - - - -
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Residues in contact with GLU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ASN* 2.9 28.0 + - + +
20C SER* 5.3 2.1 - - - +
22C ALA* 1.3 72.7 - - - +
24C PHE* 1.3 70.6 + - - +
26C MSE 3.3 2.2 + - - +
27C ARG* 2.9 66.6 + - - +
33C VAL* 4.3 23.3 - - + -
35C PRO* 4.8 7.9 - - + -
23D GLU* 2.6 24.2 - - - +
24D PHE* 4.2 1.2 - - - -
27D ARG* 2.9 23.9 + - - -
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Residues in contact with PHE 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ASN 4.8 0.2 + - - -
20C SER 5.4 3.8 + - - +
21C ALA 4.7 0.6 + - - -
23C GLU* 1.3 88.9 + - - +
25C PRO* 1.3 72.4 - - + +
27C ARG* 3.2 1.7 + - - +
28C ARG* 2.8 37.2 + - + +
268C VAL* 3.7 30.7 - - + -
269C VAL* 4.0 6.7 - - + -
272C GLN* 3.6 48.0 - - + -
275C ILE* 4.9 0.7 - - + -
23D GLU* 4.3 0.2 - - - -
24D PHE* 3.6 30.3 - + - -
27D ARG* 3.4 48.0 - - + +
28D ARG* 4.0 2.7 - - - -
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Residues in contact with PRO 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C SER 5.7 0.2 - - - +
21C ALA 3.1 22.9 - - - +
22C ALA 3.1 11.2 - - - +
24C PHE* 1.3 96.0 - - + +
26C MSE 1.4 60.9 + - - +
28C ARG* 3.3 16.1 + - + +
29C LEU* 3.3 11.3 + - - +
225C VAL* 4.2 15.0 - - + -
229C LEU* 3.5 25.5 - - + +
268C VAL* 3.9 23.6 - - + -
275C ILE* 3.9 22.3 - - + +
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Residues in contact with MSE 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 3.7 39.7 - - + -
7C ALA* 5.4 0.7 - - - -
22C ALA* 3.0 28.2 + - - +
23C GLU 3.8 0.2 - - - +
25C PRO* 1.4 75.5 - - - +
27C ARG* 1.3 60.5 + - - +
29C LEU* 3.4 9.9 + - - +
30C GLY 3.5 0.2 + - - -
31C ALA* 3.3 22.9 + - - +
33C VAL* 3.7 23.3 - - + -
80C LEU* 4.0 12.3 - - + -
228C GLY* 3.6 39.9 - - - +
229C LEU* 4.2 5.4 - - + +
231C LEU* 4.1 9.0 - - + -
232C VAL* 3.5 26.4 - - + +
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Residues in contact with ARG 27 (chain C).
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* 2.9 53.3 + - - +
26C MSE 1.3 73.0 - - - +
28C ARG* 1.3 57.3 + - - +
30C GLY 2.7 20.1 + - - -
31C ALA 3.4 18.2 - - - +
32C ASN* 5.2 0.2 - - - +
33C VAL* 2.8 39.4 + - + +
35C PRO* 4.1 13.1 - - - +
11D HIS* 6.0 0.2 - - - -
13D VAL 5.7 0.2 + - - -
15D GLY 5.3 2.2 + - - -
16D HIS* 4.1 22.5 + - - -
20D SER* 4.7 11.6 + - - +
23D GLU* 3.0 16.8 + - - -
24D PHE* 3.3 31.4 - - + +
269D VAL* 3.3 23.7 - - + +
272D GLN* 3.1 12.5 + - - -
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Residues in contact with ARG 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C PHE* 2.8 28.4 + - + +
25C PRO* 3.6 10.1 - - + +
26C MSE 3.3 0.2 - - - -
27C ARG* 1.3 76.1 - - - +
29C LEU* 1.3 60.0 + - - +
30C GLY 3.5 0.3 + - - -
272C GLN* 2.7 50.4 + - + +
273C ASP* 2.7 35.4 + - - +
275C ILE* 4.9 5.8 - - + -
276C ALA* 3.6 21.8 - - + +
24D PHE* 3.7 2.4 - - - -
28D ARG* 3.4 32.3 - - - +
272D GLN* 3.2 26.6 + - - +
273D ASP* 4.4 3.0 + - - -
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Residues in contact with LEU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C PRO 3.3 10.8 + - - +
26C MSE 3.7 9.0 - - - +
27C ARG 3.2 0.6 - - - -
28C ARG* 1.3 75.2 - - - +
30C GLY* 1.3 57.8 + - - +
31C ALA 3.7 0.2 - - - -
229C LEU* 3.5 31.6 - - + +
232C VAL* 3.9 25.1 - - + -
233C LYS* 4.1 20.2 - - + -
236C GLN* 3.4 16.9 + - - +
246C HIS* 3.5 32.5 - - + +
275C ILE* 3.8 13.7 - - + +
276C ALA* 3.9 11.7 - - - +
272D GLN* 4.7 0.2 - - - -
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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