Contacts of the helix formed by residues 15 - 27 (chain A) in PDB entry 3PRJ
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 VAL 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLY 3.0 0.6 - - - -
14A TYR* 1.3 81.7 - - + +
16A GLY* 1.3 69.0 + - - +
17A GLY 3.3 0.3 + - - -
18A PRO* 3.7 0.5 - - - +
19A THR* 3.1 26.0 + - - -
88A SER* 4.3 4.5 - - - +
129A LYS* 3.9 40.6 - - + +
130A SER* 4.9 0.7 - - - -
131A THR* 4.3 14.6 - - - +
161A GLU* 4.1 18.2 - - + -
163A LEU* 4.7 8.1 - - + -
165A GLU* 5.9 0.9 - - - +
500A NAI 3.0 40.4 + - - +
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Residues in contact with GLY 16 (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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9A CYS* 3.9 8.7 - - - -
11A GLY 3.6 20.0 - - - -
13A GLY 3.7 4.6 + - - +
15A VAL* 1.3 79.1 - - - +
17A GLY* 1.3 66.7 + - - +
19A THR* 5.1 1.8 - - - -
20A CYS* 3.0 27.5 + - - +
34A VAL* 4.8 1.6 - - - -
88A SER* 3.9 17.4 + - - -
129A LYS* 6.0 0.9 - - - -
500A NAI 4.5 1.0 + - - -
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Residues in contact with GLY 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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12A ALA* 4.1 5.4 - - - +
13A GLY 2.9 21.0 + - - +
16A GLY* 1.3 73.8 - - - +
18A PRO* 1.3 66.4 - - - +
20A CYS* 3.1 2.6 + - - +
21A SER* 3.0 26.3 + - - -
34A VAL* 4.7 7.8 - - - +
45A TRP* 3.6 21.1 - - - -
71A PHE* 4.9 2.0 - - - -
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Residues in contact with PRO 18 (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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13A GLY 3.2 15.9 - - - +
14A TYR 3.5 19.3 - - - +
15A VAL 3.7 0.9 - - - +
17A GLY* 1.3 83.8 - - - +
19A THR* 1.3 63.9 + - - +
21A SER* 3.3 2.1 + - - +
22A VAL* 3.0 28.4 + - - +
45A TRP* 3.8 7.8 - - + -
52A ILE* 3.8 16.8 - - + -
54A GLU* 5.2 2.9 - - + +
57A LEU* 3.9 27.4 - - + -
163A LEU* 5.1 0.4 - - + -
168A ALA* 4.4 15.0 - - + -
169A ILE* 4.9 1.6 - - + -
172A LEU* 3.8 13.5 - - + -
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Residues in contact with THR 19 (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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15A VAL 3.1 14.6 + - - -
16A GLY* 4.4 1.8 - - - -
18A PRO* 1.3 77.1 - - - +
20A CYS* 1.3 57.8 + - - +
22A VAL* 3.7 2.8 + - - +
23A ILE* 3.2 35.7 + - + +
86A PHE* 5.9 0.4 - - + -
129A LYS* 3.8 23.6 - - + -
161A GLU* 3.5 21.7 - - - +
163A LEU* 3.2 28.1 - - - +
172A LEU* 3.3 19.7 - - + +
199A TYR* 4.8 4.7 - - + +
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Residues in contact with CYS 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 5.3 0.9 - - - -
9A CYS* 3.4 34.5 - - - -
16A GLY* 3.0 20.6 + - - +
17A GLY 3.6 0.7 - - - +
19A THR* 1.3 75.9 - - - +
21A SER* 1.3 66.2 + - - +
22A VAL 3.1 1.8 - - - -
23A ILE* 3.0 8.6 + - - +
24A ALA* 2.9 24.8 + - - +
32A VAL* 3.8 16.2 - - + +
34A VAL* 3.5 22.0 - - + -
69A LEU* 4.2 2.5 - - - -
86A PHE* 4.4 15.7 - - - -
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Residues in contact with SER 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 GLY 3.0 18.4 + - - -
18A PRO* 3.5 11.9 - - - +
20A CYS* 1.3 74.6 - - - +
22A VAL* 1.3 62.5 + - - +
24A ALA* 3.4 3.1 + - - +
25A HIS* 3.0 22.9 + - - +
45A TRP* 4.5 0.3 - - - -
57A LEU* 4.3 2.8 - - - +
60A VAL* 3.7 15.1 - - - +
61A VAL* 3.4 31.0 - - - +
64A CYS* 4.3 2.4 - - - -
69A LEU* 3.9 19.7 - - - +
71A PHE* 4.1 5.5 - - - -
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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 PRO 3.0 19.4 + - - +
19A THR 4.1 3.6 - - - +
21A SER* 1.3 74.3 - - - +
23A ILE* 1.3 67.1 + - - +
25A HIS* 3.2 3.7 + - + +
26A MET* 3.0 36.2 + - + +
60A VAL* 4.3 11.0 - - + -
169A ILE* 3.8 33.0 - - + +
172A LEU* 3.9 37.0 - - + -
173A LYS* 4.4 11.7 - - + -
202A TRP* 4.4 9.6 - - + -
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Residues in contact with ILE 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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7A ILE* 4.6 9.2 - - + -
19A THR* 3.2 28.5 + - + +
20A CYS* 3.0 13.2 + - - +
22A VAL* 1.3 75.1 - - - +
24A ALA* 1.3 57.9 + - - +
26A MET* 3.2 1.7 + - - -
27A CYS* 2.8 36.0 + - + +
30A ILE* 5.5 1.3 - - + -
32A VAL* 4.2 15.7 - - + -
86A PHE* 3.7 34.3 - - + -
198A VAL* 4.1 25.8 - - + -
199A TYR* 5.0 7.6 - - + +
202A TRP* 4.0 23.6 - - + -
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Residues in contact with ALA 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 CYS 2.9 14.8 + - - +
21A SER 3.6 4.5 - - - +
23A ILE* 1.3 77.7 - - - +
25A HIS* 1.3 60.8 + - - +
27A CYS 3.2 10.9 + - - -
28A PRO* 3.9 1.6 - - - +
32A VAL* 3.9 19.5 - - + -
64A CYS* 3.9 7.5 - - - -
68A ASN* 2.8 30.3 + - - +
69A LEU* 3.7 29.8 - - + -
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Residues in contact with HIS 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 SER 3.0 17.4 + - - +
22A VAL* 3.2 6.0 + - - +
24A ALA* 1.3 75.6 - - - +
26A MET* 1.3 78.1 + - - +
27A CYS 3.5 0.2 - - - -
28A PRO* 4.9 6.6 - - - +
60A VAL* 4.1 17.7 - - + +
63A SER* 3.3 24.4 + - - -
64A CYS* 3.6 13.0 - - - +
173A LYS* 4.2 25.1 + - - -
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Residues in contact with MET 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* 3.0 20.7 + - + +
23A ILE 4.0 1.8 - - - +
25A HIS* 1.3 94.3 - - + +
27A CYS* 1.3 63.4 + - - +
28A PRO* 3.8 8.4 - - - +
173A LYS* 3.6 39.5 - - + +
201A HIS* 3.9 13.5 - - - +
202A TRP* 3.5 63.3 - - + +
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Residues in contact with CYS 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 ILE* 2.8 22.0 + - + +
24A ALA* 3.2 4.5 + - - +
26A MET* 1.3 81.9 - - - +
28A PRO* 1.4 67.4 - - - +
29A GLU* 3.0 9.6 + - - +
30A ILE* 3.1 34.7 + - + +
68A ASN* 3.3 7.6 + - - -
198A VAL* 3.7 28.0 - - - -
201A HIS* 3.6 28.0 - - + -
202A TRP* 4.3 4.7 - - - -
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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