Contacts of the helix formed by residues 19 - 28 (chain A) in PDB entry 4YVG
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 PHE 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LYS* 3.3 31.4 - - + -
15A ALA* 3.6 20.2 - - - +
16A ILE 3.8 1.7 + - - +
17A THR 3.7 0.8 - - - -
18A GLU* 1.3 104.2 - - + +
20A GLY* 1.3 66.9 + - - +
22A THR* 3.3 10.4 + - - -
23A GLY* 3.1 12.8 + - - -
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Residues in contact with GLY 20 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PHE* 1.3 73.2 - - - +
21A VAL* 1.3 66.4 + - - -
23A GLY* 3.2 0.7 + - - -
24A ARG* 3.0 31.7 + - - +
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Residues in contact with VAL 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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20A GLY* 1.3 71.8 - - - -
22A THR* 1.3 62.8 + - + +
24A ARG* 3.4 23.3 + - - +
25A ALA* 2.9 26.5 + - - +
154A ARG* 5.8 3.1 - - + -
159A VAL* 3.3 41.6 - - + +
160A LEU* 3.9 18.8 - - + -
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Residues in contact with THR 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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16A ILE* 2.7 37.0 + - + +
19A PHE 3.3 6.9 + - - -
21A VAL* 1.3 83.4 - - + +
23A GLY* 1.3 57.1 + - - +
25A ALA* 3.2 8.7 + - - +
26A VAL* 3.0 31.5 + - - +
31A LEU* 4.6 7.1 - - + +
149A ILE* 5.5 1.1 - - + -
150A ASP* 3.5 40.2 + - + +
153A ALA* 4.2 15.3 - - + -
154A ARG* 6.4 0.9 - - + -
159A VAL* 5.4 0.2 - - - -
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Residues in contact with GLY 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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16A ILE 3.2 6.1 + - - -
17A THR 3.3 24.6 - - - +
18A GLU 4.1 1.6 - - - -
19A PHE 3.1 22.9 + - - -
20A GLY 3.2 1.5 + - - -
22A THR* 1.3 72.8 - - - +
24A ARG* 1.3 66.1 + - - +
26A VAL* 3.2 2.6 + - - +
27A LYS* 2.9 24.3 + - - +
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Residues in contact with ARG 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 GLY* 3.0 13.0 + - - +
21A VAL* 3.7 38.0 - - - +
22A THR 3.2 0.2 - - - -
23A GLY* 1.3 77.5 - - - +
25A ALA* 1.3 63.1 + - - +
27A LYS* 4.5 4.9 - - - +
28A HIS* 2.9 55.4 + - + +
30A LEU* 6.3 1.1 - - + -
159A VAL 5.2 6.1 + - - +
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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 VAL 2.9 15.2 + - - +
22A THR* 3.2 12.8 + - - +
24A ARG* 1.3 77.0 - - - +
26A VAL* 1.3 58.6 + - - +
28A HIS 3.6 0.3 + - - -
29A ASN 3.3 2.4 + - - -
30A LEU* 2.9 41.0 + - + -
31A LEU* 3.2 18.9 + - + -
153A ALA* 5.5 1.1 - - + -
159A VAL* 3.8 30.5 - - + +
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Residues in contact with VAL 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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16A ILE* 4.7 0.9 - - + +
17A THR* 3.9 42.2 - - + +
22A THR 3.0 18.5 + - - +
23A GLY 3.6 6.3 - - - +
25A ALA* 1.3 74.0 - - - +
27A LYS* 1.3 66.4 + - - +
29A ASN* 3.0 18.0 + - - +
31A LEU* 3.4 35.7 - - + +
32A LYS* 5.5 1.1 - - - +
33A VAL* 4.5 7.9 - - + +
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Residues in contact with LYS 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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17A THR 5.2 0.2 + - - -
23A GLY 2.9 17.3 + - - +
24A ARG* 3.9 5.6 - - - +
26A VAL* 1.3 77.0 - - - +
28A HIS* 1.3 74.1 + - + +
29A ASN* 3.4 10.2 + - - +
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Residues in contact with HIS 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 ARG* 2.9 48.9 + - + +
25A ALA 4.2 2.2 - - - +
27A LYS* 1.3 91.6 - - + +
29A ASN* 1.3 74.3 + - - +
30A LEU* 3.2 23.4 + - + +
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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
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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