Contacts of the helix formed by residues 9 - 29 (chain B) in PDB entry 4PKO
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 9 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PHE* 1.3 73.6 - - - +
10B ASN* 1.3 64.3 + - - -
12B ALA* 2.9 15.3 + - - +
13B ARG* 2.9 27.2 + - - +
517B THR 5.1 0.9 - - - +
518B GLU* 2.9 37.9 + - - -
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Residues in contact with ASN 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE 3.7 0.2 + - - -
9B GLY* 1.3 71.6 - - - -
11B ASP* 1.3 61.8 + - - +
13B ARG* 3.0 25.1 + - - +
14B VAL* 3.0 46.0 + - - +
104B LEU 5.4 0.7 - - - +
108B ALA* 4.0 23.7 - - - +
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Residues in contact with ASP 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LYS* 3.5 36.5 + - - +
8B PHE 3.2 14.3 + - - +
9B GLY 3.0 0.2 - - - -
10B ASN* 1.3 79.8 - - - +
12B ALA* 1.3 60.5 + - - +
14B VAL* 3.8 4.2 + - - +
15B LYS* 3.6 18.9 + - - +
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Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LYS* 3.7 38.8 - - + +
8B PHE* 3.3 2.8 + - - -
9B GLY 2.9 8.9 + - - +
11B ASP* 1.3 77.4 - - - +
13B ARG* 1.3 67.9 + - - +
14B VAL 3.2 0.2 - - - -
15B LYS* 3.1 9.4 + - - +
16B MET 2.9 18.4 + - - -
66B PHE* 6.1 0.7 - - + -
517B THR* 5.9 1.1 - - + +
518B GLU 5.4 0.2 - - - -
519B CYS* 5.0 2.9 - - - +
520B MET* 3.7 28.9 - - + +
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Residues in contact with ARG 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLY* 2.9 18.9 + - - +
10B ASN* 3.0 42.1 + - - +
11B ASP 3.5 0.2 - - - -
12B ALA* 1.3 76.3 - - - +
14B VAL* 1.3 53.6 + - + +
16B MET* 3.1 16.3 + - + +
17B LEU* 2.7 35.0 + - - +
104B LEU* 3.3 42.0 + - + +
107B VAL* 4.1 24.3 + - - +
108B ALA* 5.6 1.6 - - - +
113B PRO* 5.9 0.6 - - - +
514B MET 5.8 0.2 - - - +
515B ILE 5.2 3.2 + - - -
516B THR 5.6 0.4 - - - -
517B THR* 2.8 38.6 + - + +
518B GLU* 2.8 25.9 + - - +
520B MET* 5.4 0.2 - - - -
36C ARG* 4.0 10.7 - - - +
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Residues in contact with VAL 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASN* 3.0 35.9 + - - +
11B ASP* 4.0 4.9 - - - +
12B ALA 3.2 0.6 - - - -
13B ARG* 1.3 74.7 - - + +
15B LYS* 1.3 57.7 + - + +
17B LEU* 3.0 15.8 + - + +
18B ARG* 2.7 50.9 + - + +
104B LEU* 5.7 0.2 - - - -
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Residues in contact with LYS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LYS* 3.2 28.9 - - + +
11B ASP* 3.6 12.7 + - - +
12B ALA* 3.1 9.9 + - - +
14B VAL* 1.3 79.6 - - + +
16B MET* 1.3 63.9 + - - +
18B ARG* 4.7 4.9 - - - +
19B GLY 3.3 3.6 + - - -
64B ASP* 3.2 29.2 + - - +
66B PHE* 3.6 28.9 - - + -
67B GLU* 3.0 47.4 - - + +
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Residues in contact with MET 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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12B ALA 2.9 12.2 + - - +
13B ARG* 3.1 13.9 - - + +
15B LYS* 1.3 76.1 - - - +
17B LEU* 1.3 62.3 + - - +
19B GLY* 3.2 4.3 + - - -
20B VAL* 3.0 24.4 + - + +
66B PHE 4.3 10.0 + - - -
70B GLY* 3.7 21.1 - - - +
73B MET* 4.1 8.7 - - + -
100B ILE* 4.6 9.0 - - + -
104B LEU* 4.3 28.3 - - + -
514B MET* 3.3 48.2 - - + +
517B THR* 3.9 17.9 - - - +
520B MET* 4.0 12.2 - - - +
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Residues in contact with LEU 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 ARG 2.7 16.6 + - - +
14B VAL* 3.0 20.4 + - + +
16B MET* 1.3 72.2 - - - +
18B ARG* 1.3 67.2 + - + +
20B VAL* 3.0 12.1 + - + +
21B ASN* 2.9 42.9 + - - +
100B ILE* 4.5 11.4 - - + -
101B THR* 4.1 23.8 - - + +
104B LEU* 3.9 26.5 - - + -
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Residues in contact with ARG 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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14B VAL* 2.7 37.2 + - + +
15B LYS* 3.9 5.2 - - - +
17B LEU* 1.3 74.0 - - + +
19B GLY* 1.3 61.6 + - - +
21B ASN* 3.6 10.8 + - - +
22B VAL* 3.4 31.0 + - - +
67B GLU* 2.9 43.8 + - - +
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Residues in contact with GLY 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS 3.3 4.6 + - - -
16B MET 3.2 4.5 + - - -
17B LEU 3.0 0.8 - - - -
18B ARG* 1.3 76.5 - - - +
20B VAL* 1.3 64.2 + - - +
22B VAL* 3.2 13.0 + - - +
23B LEU 3.3 9.2 + - - -
62B LEU* 3.7 12.1 - - - +
67B GLU* 3.2 27.5 - - - +
71B ALA* 3.5 15.4 - - - +
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Residues in contact with VAL 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 MET* 3.0 17.5 + - + +
17B LEU* 3.0 15.1 + - + +
19B GLY* 1.3 74.0 - - - +
21B ASN* 1.3 59.2 + - - +
23B LEU* 3.3 3.3 + - - +
24B ALA* 2.9 28.0 + - + +
70B GLY* 3.7 14.4 - - - +
71B ALA 4.1 0.8 - - - +
74B VAL* 3.7 41.8 - - + +
97B GLN* 4.8 19.5 - - + -
100B ILE* 4.1 22.9 - - + -
514B MET* 4.4 4.3 - - - -
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Residues in contact with ASN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 2.9 43.7 + - - +
18B ARG* 3.7 10.9 - - - +
20B VAL* 1.3 76.9 - - - +
22B VAL* 1.3 57.6 + - + +
25B ASP* 2.8 45.1 + - - +
97B GLN* 3.3 26.7 + - - +
101B THR* 4.5 7.5 + - - -
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 4.0 30.7 - - + -
8A PHE* 4.8 3.7 - - + -
18B ARG* 3.4 18.8 + - - +
19B GLY 3.2 8.6 + - - +
21B ASN* 1.3 76.6 - - + +
23B LEU* 1.3 67.7 + - - +
25B ASP* 4.0 4.0 - - - +
26B ALA* 3.2 24.1 + - - +
60B ILE* 4.5 5.6 - - + -
62B LEU* 4.0 31.0 - - + -
67B GLU* 5.6 2.5 - - - +
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Residues in contact with LEU 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 GLY 3.3 2.8 + - - -
20B VAL 3.7 6.7 - - - +
22B VAL* 1.3 80.5 - - - +
24B ALA* 1.3 62.4 + - - +
26B ALA* 3.7 2.9 + - - +
27B VAL* 3.3 19.6 + - + +
57B ALA* 3.4 45.8 - - + +
60B ILE* 3.4 28.4 - - + +
71B ALA* 3.8 31.2 - - + +
74B VAL* 4.0 18.2 - - + +
75B LYS* 4.4 12.3 - - + -
78B ALA* 5.3 0.2 - - + -
93B THR* 4.3 17.9 - - + +
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Residues in contact with ALA 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 VAL* 2.9 18.9 + - + +
21B ASN 3.8 0.4 - - - +
23B LEU* 1.3 75.9 - - + +
25B ASP* 1.3 54.9 + - - +
26B ALA 3.1 1.8 - - - -
27B VAL* 2.8 8.3 + - - +
28B LYS* 2.8 37.1 + - + +
93B THR* 3.9 18.8 - - + -
97B GLN* 3.6 41.5 - - + +
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Residues in contact with ASP 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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8A PHE* 3.3 25.3 - - + -
21B ASN* 2.8 37.0 + - - +
22B VAL* 4.0 4.6 - - - +
24B ALA* 1.3 72.2 - - - +
26B ALA* 1.3 59.9 + - - +
28B LYS* 3.1 38.1 + - - +
29B VAL* 4.0 13.9 + - - +
97B GLN* 3.5 10.5 + - - -
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Residues in contact with ALA 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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6A VAL* 5.3 2.5 - - + -
8A PHE* 3.7 18.8 - - + -
519A CYS* 4.3 10.3 - - - -
521A VAL* 5.2 1.8 - - + -
22B VAL 3.2 16.0 + - - +
23B LEU 4.0 3.4 - - - +
24B ALA 3.0 1.0 + - - -
25B ASP* 1.3 76.9 - - - +
27B VAL* 1.3 59.8 + - - +
29B VAL* 3.3 19.5 - - - +
30B THR* 4.3 0.2 - - - +
38B VAL* 3.4 13.5 - - - +
56B VAL* 3.7 19.8 - - + +
60B ILE* 4.4 14.4 - - + -
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Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 3.3 19.7 + - + +
24B ALA 2.8 8.2 + - - +
26B ALA* 1.3 76.0 - - - +
28B LYS* 1.3 63.5 + - - +
29B VAL 3.2 4.6 + - - -
30B THR* 3.2 21.7 + - - +
53B GLY* 3.8 24.5 - - - +
56B VAL* 3.9 13.9 - - + -
57B ALA* 4.0 15.7 - - + -
89B THR 5.1 0.2 - - - +
90B THR* 3.4 35.7 - - + +
93B THR* 4.0 19.3 - - + +
94B VAL* 5.9 0.4 - - + -
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Residues in contact with LYS 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 ALA* 2.8 22.6 + - + +
25B ASP* 3.1 36.3 + - - +
26B ALA 3.5 0.6 - - - -
27B VAL* 1.3 74.9 - - + +
29B VAL* 1.3 63.2 + - + +
30B THR 3.0 2.4 + - - -
31B LEU* 3.0 20.6 + - - +
90B THR* 4.6 4.7 - - - -
93B THR* 5.8 0.4 - - + -
94B VAL* 4.1 19.3 - - + -
97B GLN* 3.5 23.5 + - - +
453B GLN* 3.4 42.5 - - + +
456B LEU* 5.8 0.6 - - - +
457B ASN* 3.4 7.6 + - - -
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 4.8 7.6 - - + -
518A GLU* 3.5 38.6 - - + -
519A CYS* 4.5 4.0 - - + -
25B ASP 4.0 12.8 - - - +
26B ALA 3.3 23.3 - - - +
28B LYS* 1.3 76.9 - - + +
30B THR* 1.3 50.9 + - + +
31B LEU 3.3 1.3 - - - -
35B GLY* 3.3 5.8 - - - -
36B ARG* 2.5 36.3 + - + +
38B VAL* 3.4 21.1 - - + -
457B ASN* 4.2 12.2 + - - +
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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
------------------------------------------------------------
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