Contacts of the helix formed by residues 14 - 30 (chain B) in PDB entry 2DPD
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 LYS 14 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A PHE* 4.0 0.4 - - - -
8B SER* 6.1 5.8 - - - -
11B PHE* 6.0 5.6 - - - +
12B LEU 3.5 20.7 + - - +
13B VAL* 1.3 83.9 - - - +
15B GLN* 1.3 64.7 + - - +
16B ARG* 3.4 22.2 - - + +
17B ALA* 3.4 6.8 + - + +
18B PHE* 3.1 19.2 + - - +
106B GLU* 4.9 3.0 + - - +
13D T 5.2 13.3 + - - -
12E A 3.7 37.0 + - - +
13E T 3.3 22.6 + - - +
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Residues in contact with GLN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A THR* 3.8 4.8 + - - -
11A PHE* 3.6 43.7 - - + +
14B LYS* 1.3 68.9 - - - +
16B ARG* 1.3 67.9 + - - +
18B PHE* 2.9 5.5 + - - +
19B LEU* 2.9 28.3 + - + +
50B PHE* 3.9 23.0 - - + -
52B PRO* 4.1 9.7 - - - +
56B GLU* 3.6 22.3 - - - +
13E T 2.6 30.4 + - - +
14E G 3.2 33.4 + - - -
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Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LYS* 4.4 16.4 - - + +
15B GLN* 1.3 78.3 - - - +
17B ALA* 1.3 57.4 + - - +
19B LEU* 3.4 3.1 + - - +
20B LYS* 2.7 51.1 + - - +
56B GLU* 4.1 11.4 + - - +
59B ARG* 6.0 0.9 - - + -
60B SER* 3.8 21.5 + - - +
63B GLU* 3.3 41.9 + - - +
99B TYR* 5.5 0.2 - - - -
12E A 3.2 37.4 + - + +
13E T 3.3 16.2 + - - +
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Residues in contact with ALA 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B VAL* 3.8 10.3 - - + -
14B LYS* 3.4 15.3 + - + +
15B GLN 3.1 0.6 - - - -
16B ARG* 1.3 80.3 - - - +
18B PHE* 1.3 69.0 + - - +
20B LYS* 3.0 1.3 + - - +
21B LEU* 2.8 26.3 + - - +
99B TYR* 3.9 16.6 - - - +
103B LEU* 3.4 27.7 - - + +
106B GLU* 4.7 5.4 - - - +
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Residues in contact with PHE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 3.5 37.2 - + + -
113A LEU* 4.1 19.7 - - + -
114A ILE* 4.9 4.7 - - + -
117A ALA* 3.4 34.5 - - + -
13B VAL* 4.3 9.1 - - + +
14B LYS 3.1 4.8 + - - +
15B GLN 2.9 8.9 + - - +
17B ALA* 1.3 80.3 - - - +
19B LEU* 1.3 70.3 + - + +
21B LEU* 3.4 8.4 - - + +
22B TYR* 3.3 36.7 + + - -
45B PHE* 3.7 24.0 - + - -
50B PHE* 3.9 17.5 - + - -
103B LEU* 5.6 0.4 - - - -
107B LEU* 4.6 14.1 - - + -
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLN* 2.9 25.4 + - + +
16B ARG 3.8 1.1 - - - +
18B PHE* 1.3 76.1 - - + +
20B LYS* 1.3 69.9 + - - +
22B TYR* 2.8 18.7 + - + +
23B MET* 2.9 24.0 + - + +
37B LEU* 5.3 0.2 - - + -
41B LEU* 3.5 29.4 - - + -
50B PHE* 4.2 22.0 - - + -
52B PRO* 4.6 5.6 - - + -
56B GLU* 3.8 25.8 - - + -
57B VAL* 4.0 19.1 - - + +
60B SER* 3.4 25.1 - - - +
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Residues in contact with LYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ARG* 2.7 44.6 + - - +
17B ALA 3.0 2.9 + - - +
19B LEU* 1.3 71.9 - - - +
21B LEU* 1.3 67.2 + - - +
23B MET* 3.1 9.3 + - - +
24B ILE* 3.0 27.3 + - - +
60B SER* 3.7 24.0 - - - +
63B GLU* 2.8 32.6 + - + +
64B LEU* 3.6 28.9 - - + +
67B ASP* 3.9 15.6 + - - -
99B TYR* 3.2 38.7 + - + +
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ALA* 4.7 3.1 - - + +
121A ASN* 2.9 37.0 + - + +
122A PHE* 3.7 23.6 - - + -
17B ALA 2.8 11.7 + - - +
18B PHE* 3.4 13.7 - - - +
20B LYS* 1.3 78.4 - - - +
22B TYR* 1.3 62.7 + - + +
24B ILE* 2.9 14.9 + - + +
25B THR* 3.1 13.7 + - - -
100B LYS* 3.6 34.3 - - + -
103B LEU* 3.9 26.9 - - + +
107B LEU* 3.7 21.1 - - + -
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Residues in contact with TYR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ALA* 3.2 22.0 + - + -
120A ASP* 2.6 32.9 + - + -
121A ASN* 3.3 28.6 - - - +
18B PHE* 3.3 48.6 + + - +
19B LEU* 2.8 15.1 + - - +
21B LEU* 1.3 76.4 - - + +
23B MET* 1.3 60.6 + - - +
25B THR* 3.5 2.9 + - - -
26B MET* 3.0 42.9 + - + +
37B LEU* 4.4 6.5 - - + -
41B LEU* 3.8 27.6 - - + -
44B GLU* 3.8 11.9 - - - -
45B PHE* 3.2 17.6 - + - -
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Residues in contact with MET 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 2.9 43.5 + - + +
20B LYS* 3.5 10.3 - - - +
22B TYR* 1.3 72.5 - - - +
24B ILE* 1.3 56.1 + - - +
26B MET* 3.2 2.0 + - - +
27B THR* 2.7 41.5 + - - +
32B LEU* 6.0 0.6 - - - +
37B LEU* 3.6 34.3 - - + +
57B VAL* 3.4 8.7 - - + +
60B SER* 3.3 25.1 - - - +
61B LEU* 2.4 49.1 - - + -
64B LEU* 4.0 11.0 - - + -
70B LEU* 5.0 4.5 - - + -
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Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LYS 3.0 18.7 + - - +
21B LEU* 2.9 10.4 + - + +
23B MET* 1.3 80.6 - - - +
25B THR* 1.3 61.4 + - - +
27B THR* 3.4 7.7 + - - -
28B GLU* 3.2 22.3 + - - +
64B LEU* 3.7 22.4 - - + -
69B ILE* 4.7 12.6 - - + -
70B LEU* 5.5 2.5 - - + -
90B PHE* 3.6 11.3 - - + -
93B TYR* 5.8 0.2 - - + -
96B ALA* 4.2 20.9 - - + +
99B TYR* 3.4 35.0 - - + -
100B LYS* 3.7 29.4 - - + +
103B LEU* 4.8 1.6 - - + -
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Residues in contact with THR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ASP 4.6 4.7 - - - +
121A ASN* 2.4 47.6 + - - +
21B LEU 3.1 4.2 + - - -
22B TYR* 4.0 2.7 - - - -
24B ILE* 1.3 76.9 - - - +
26B MET* 1.3 61.2 + - - +
28B GLU* 3.0 44.4 + - - +
29B GLN* 3.4 21.5 + - - +
100B LYS* 3.4 18.2 - - - +
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Residues in contact with MET 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ASP* 6.1 2.5 - - + -
22B TYR* 3.0 37.0 + - + +
23B MET* 4.1 2.2 - - - +
25B THR* 1.3 75.7 - - - +
27B THR* 1.3 61.9 + - - +
29B GLN* 2.9 18.7 + - - +
30B GLU* 2.8 36.7 + - + +
32B LEU* 3.5 28.9 - - + -
37B LEU* 4.2 16.4 - - + -
40B VAL* 4.6 15.0 - - + -
41B LEU* 5.3 1.3 - - - -
44B GLU* 3.8 24.7 - - - +
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Residues in contact with THR 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B MET* 2.7 27.2 + - - +
24B ILE* 3.5 5.8 - - - -
26B MET* 1.3 72.2 - - - +
28B GLU* 1.3 64.6 + - - +
29B GLN 3.0 0.9 + - - -
30B GLU 3.3 16.3 + - - +
32B LEU* 5.3 5.6 + - - +
70B LEU* 4.2 20.5 - - + +
88B TYR* 4.0 22.4 + - - +
89B GLN* 4.3 6.5 - - - -
90B PHE* 3.6 30.1 - - + -
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 3.2 17.2 + - - +
25B THR* 3.0 22.9 + - - +
27B THR* 1.3 80.8 - - - +
29B GLN* 1.3 62.2 + - + +
90B PHE* 3.9 16.6 - - + -
93B TYR* 3.0 31.6 + - + +
97B LYS* 5.4 3.5 - - - +
100B LYS* 3.3 35.6 + - - +
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Residues in contact with GLN 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B THR* 3.4 25.9 + - - +
26B MET* 2.9 25.0 + - - +
27B THR 4.3 0.4 - - - -
28B GLU* 1.3 86.0 - - + +
30B GLU* 1.3 69.4 + - + +
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B MET* 2.8 23.7 + - + +
27B THR* 3.3 17.5 - - - +
29B GLN* 1.3 83.6 - - + +
31B ARG* 1.3 72.3 + - - +
32B LEU* 3.8 16.7 + - + -
36B LYS* 4.8 6.7 - - - +
77B LYS* 5.1 8.2 + - - +
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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
------------------------------------------------------------
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