Contacts of the helix formed by residues 14 - 30 (chain A) in PDB entry 1RPJ
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 PRO 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A SER 4.1 5.4 - - - +
13A ASN* 1.3 89.4 - - - +
15A PHE* 1.3 55.1 + - - +
17A VAL* 3.1 14.4 + - + +
18A ASP* 2.8 39.4 + - - +
203A THR* 5.9 0.2 - - - +
229A ILE* 3.7 24.9 - - + -
230A PRO* 3.6 29.2 - - + -
231A GLU* 6.0 0.9 - - + +
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Residues in contact with PHE 15 (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 ASN* 3.0 17.2 + - - +
14A PRO* 1.3 76.2 - - - +
16A TRP* 1.3 82.8 + + - +
18A ASP* 4.8 0.9 - - - -
19A MET* 3.1 43.7 + - + +
91A ASP* 3.5 17.5 - - - -
227A ASP* 3.9 26.9 - - + +
229A ILE* 3.9 7.5 - - + +
247A GLN* 3.3 32.5 - - + -
249A PRO* 3.1 46.9 - - + +
252A ILE* 4.2 4.0 - - + -
291A ALL 3.6 22.0 - - - -
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Residues in contact with TRP 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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8A LEU* 3.6 22.2 - - + +
9A LYS* 3.3 35.8 - - + +
10A THR* 3.1 41.5 - - + +
11A LEU* 3.9 6.5 - - + -
13A ASN* 3.0 21.5 + - + +
15A PHE* 1.3 88.9 - + - +
17A VAL* 1.3 63.8 + - - +
19A MET* 3.2 31.9 + - + -
20A LYS* 3.0 20.3 + - - +
66A ALA* 3.4 32.1 - - + -
91A ASP* 3.3 31.4 - - + -
291A ALL 3.0 22.2 + - - -
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Residues in contact with VAL 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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11A LEU* 3.2 42.6 - - + +
13A ASN 3.3 7.9 + - - +
14A PRO* 3.1 15.2 + - + +
16A TRP* 1.3 76.1 - - - +
18A ASP* 1.3 68.1 + - - +
20A LYS* 3.3 6.0 + - + +
21A LYS* 3.3 23.5 + - + +
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Residues in contact with ASP 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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14A PRO* 2.8 26.0 + - - +
15A PHE* 4.9 0.5 - - - -
17A VAL* 1.3 81.6 - - - +
19A MET* 1.3 66.4 + - - +
21A LYS* 3.5 8.8 + - - +
22A GLY 3.0 18.5 + - - -
228A GLY 5.8 0.2 - - - +
229A ILE* 5.9 0.7 - - - -
230A PRO* 5.1 9.3 - - - +
249A PRO* 3.8 20.1 - - + +
250A ALA* 3.6 16.1 - - + +
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Residues in contact with MET 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.8 13.5 - - + -
15A PHE* 3.1 36.1 + - + +
16A TRP* 3.2 43.0 + - + +
18A ASP* 1.3 76.5 - - - +
20A LYS* 1.3 61.7 + - - +
22A GLY* 3.2 2.3 + - - -
23A ILE* 3.0 26.9 + - + +
90A LEU* 4.0 16.4 - - - -
91A ASP* 4.2 3.8 - - + -
249A PRO* 3.2 23.9 - - + +
252A ILE* 3.6 25.1 - - + -
253A GLY* 3.6 15.3 - - - -
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Residues in contact with LYS 20 (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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8A LEU* 3.7 12.7 - - + +
11A LEU* 3.9 30.5 - - + -
16A TRP 3.0 12.7 + - - +
17A VAL* 3.4 10.1 - - - +
19A MET* 1.3 75.0 - - - +
21A LYS* 1.3 56.8 + - - +
23A ILE* 3.2 5.1 + - - +
24A GLU* 2.6 65.0 + - - +
36A ILE* 3.7 36.1 - - + +
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Residues in contact with LYS 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 VAL* 3.3 12.7 + - + +
18A ASP* 3.7 11.7 - - - +
20A LYS* 1.3 79.2 - - - +
22A GLY* 1.3 56.6 + - - +
24A GLU* 3.2 19.7 + - - +
25A ASP* 2.8 52.0 + - - +
250A ALA* 6.2 0.7 - - + -
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Residues in contact with GLY 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 ASP 3.0 11.3 + - - -
19A MET 3.2 2.2 + - - -
21A LYS* 1.3 74.8 - - - +
23A ILE* 1.3 57.8 + - - +
25A ASP* 3.4 7.8 + - - +
26A GLU* 2.9 30.3 + - - +
250A ALA* 3.6 34.1 - - - +
254A ALA* 3.8 5.4 - - - +
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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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6A VAL* 3.6 44.0 - - + -
8A LEU* 4.1 12.3 - - + -
19A MET* 3.0 16.3 + - + +
20A LYS* 3.5 9.6 - - - +
22A GLY* 1.3 73.4 - - - +
24A GLU* 1.3 59.7 + - - +
26A GLU* 3.2 6.2 + - - -
27A ALA* 2.8 28.4 + - - +
34A VAL* 4.1 7.2 - - + -
36A ILE* 3.7 16.4 - - + -
90A LEU* 4.3 5.8 - - + -
253A GLY* 3.5 31.0 - - - +
254A ALA 4.3 0.4 - - - +
257A LEU* 3.6 17.9 - - + +
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Residues in contact with GLU 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 LYS* 2.6 56.7 + - - +
21A LYS* 3.2 25.1 + - + +
23A ILE* 1.3 75.7 - - - +
25A ASP* 1.3 66.3 + - - +
27A ALA* 3.3 8.4 + - - +
28A LYS* 3.3 31.8 + - + +
34A VAL* 6.4 0.4 - - - -
36A ILE* 3.5 16.3 - - + +
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Residues in contact with ASP 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 LYS* 2.8 38.4 + - - +
22A GLY* 3.7 6.9 - - - +
24A GLU* 1.3 80.1 - - - +
26A GLU* 1.3 61.7 + - - +
28A LYS* 3.3 24.0 + - - +
29A THR* 3.2 23.1 + - - -
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Residues in contact with GLU 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 GLY 2.9 17.8 + - - +
23A ILE 3.7 3.6 - - - +
25A ASP* 1.3 73.1 - - - +
27A ALA* 1.3 66.0 + - - +
29A THR* 3.0 15.1 + - - +
30A LEU* 2.9 56.0 + - + +
254A ALA* 3.3 40.3 - - + +
257A LEU* 3.9 6.3 - - + -
258A LYS* 3.7 13.6 - - - +
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Residues in contact with ALA 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 17.3 + - - +
24A GLU* 3.5 9.6 - - - +
26A GLU* 1.3 75.8 - - - +
28A LYS* 1.3 53.8 + - + +
30A LEU 3.3 0.5 + - - -
31A GLY* 2.7 31.0 + - - -
32A VAL* 3.0 31.3 + - - +
34A VAL* 3.7 22.2 - - + +
257A LEU* 3.5 8.5 - - + +
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Residues in contact with LYS 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 GLU* 3.3 19.3 + - - +
25A ASP* 3.5 21.5 + - - +
26A GLU 3.2 0.2 - - - -
27A ALA* 1.3 81.0 - - + +
29A THR* 1.4 63.2 + - - +
31A GLY* 3.3 12.2 + - - -
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Residues in contact with THR 29 (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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25A ASP 3.2 12.1 + - - -
26A GLU* 3.0 27.0 + - - +
28A LYS* 1.4 78.8 - - - +
30A LEU* 1.3 65.9 + - + +
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Residues in contact with LEU 30 (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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26A GLU* 2.9 40.1 + - + +
27A ALA 4.0 2.0 - - - +
29A THR* 1.3 84.9 - - + +
31A GLY* 1.3 61.0 - - - +
32A VAL* 4.1 17.6 - - + +
257A LEU* 4.2 5.4 - - + -
258A LYS* 3.4 59.5 - - + +
261A VAL* 4.0 23.3 - - + +
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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