Contacts of the helix formed by residues 11 - 29 (chain I) in PDB entry 1Q0K
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 11 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I ASP* 1.3 86.1 - - - +
12I ALA* 1.3 56.0 + - - -
13I GLN 3.2 0.4 - - - -
14I ALA* 3.0 10.8 + - + +
15I ARG* 2.9 28.5 + - - +
54I HIS* 6.5 0.2 - - + -
55I LEU* 5.8 0.4 - - + -
58I LEU* 3.7 27.6 - - + -
104I ILE* 4.4 9.5 - - + +
107I ILE* 5.0 2.9 - - + +
108I ASP* 3.8 30.1 - - + +
111I PHE* 3.4 46.7 - - + -
112I TRP* 5.0 0.9 - - - +
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Residues in contact with ALA 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G ALA* 5.9 2.5 - - + -
15G ARG* 6.1 0.9 - - - +
16G ILE* 4.2 9.2 - - + -
10I ASP* 2.7 31.5 + - - +
11I PRO* 1.3 70.4 - - - +
13I GLN* 1.3 63.8 + - - +
15I ARG* 3.7 32.8 - - - +
16I ILE* 2.9 37.9 + - + +
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Residues in contact with GLN 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G GLN* 5.4 7.8 + - + +
16G ILE* 3.8 33.3 - - + +
17G GLU* 3.0 27.7 + - - +
1I HIS* 3.5 31.9 + - - +
10I ASP 3.0 19.1 + - - +
12I ALA* 1.3 78.6 - - - +
14I ALA* 1.3 63.2 + - - +
16I ILE* 3.6 6.1 + - - +
17I GLU* 3.5 25.8 + - - +
54I HIS* 3.6 37.0 + - + +
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Residues in contact with ALA 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I ASP 4.5 0.2 + - - -
11I PRO* 3.0 12.7 + - + +
13I GLN* 1.3 77.7 - - - +
15I ARG* 1.3 64.9 + - - +
17I GLU* 3.4 4.0 + - - +
18I ALA* 3.1 22.9 + - - +
51I ALA* 3.9 8.8 - - - +
54I HIS* 3.7 26.5 - - + +
55I LEU* 3.8 30.7 - - + -
58I LEU* 5.6 0.4 - - + -
104I ILE* 3.9 9.4 - - + +
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Residues in contact with ARG 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I ASP* 5.4 0.2 + - - -
11I PRO 2.9 11.5 + - - +
12I ALA* 3.2 30.4 + - - +
14I ALA* 1.3 77.2 - - - +
16I ILE* 1.3 63.0 + - - +
18I ALA* 3.1 3.2 + - - +
19I GLU* 2.9 54.0 + - - +
101I LEU* 4.0 13.5 - - + +
104I ILE* 4.0 21.6 - - + +
105I ALA* 6.5 1.1 - - - +
108I ASP* 3.7 24.2 + - - +
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Residues in contact with ILE 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G HIS* 4.1 11.9 - - + +
8G VAL* 3.8 18.2 - - + +
9G TYR 5.6 0.9 - - - -
10G ASP* 4.2 26.7 - - + +
12G ALA* 4.4 13.9 - - + -
13G GLN* 4.0 32.3 - - + +
16G ILE* 5.8 1.1 - - + -
12I ALA* 2.9 26.5 + - + +
13I GLN* 4.1 5.6 - - - +
15I ARG* 1.3 82.9 - - + +
17I GLU* 1.3 62.0 + - - +
19I GLU* 3.3 15.8 + - - +
20I SER* 3.3 21.0 + - - -
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Residues in contact with GLU 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G HIS* 3.3 9.4 + - - -
13G GLN* 3.2 20.3 + - - +
7007G THJ 3.7 4.9 - - - -
13I GLN 3.5 13.9 + - - +
14I ALA 3.4 7.7 + - - +
15I ARG 3.3 0.6 - - - -
16I ILE* 1.3 75.3 - - - +
18I ALA* 1.3 64.3 + - - +
20I SER* 3.3 5.7 + - - -
21I VAL* 3.2 25.8 + - - +
47I ARG* 2.9 62.8 + - - +
50I LEU* 3.8 20.0 - - + +
51I ALA* 3.9 6.3 - - + -
54I HIS* 4.2 11.1 + - + +
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Residues in contact with ALA 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ALA 3.1 14.4 + - - +
15I ARG 3.4 7.9 - - - +
17I GLU* 1.3 78.1 - - - +
19I GLU* 1.3 61.7 - - - +
21I VAL* 3.3 13.0 - - - +
22I LYS* 3.2 20.3 + - - +
51I ALA* 4.3 3.3 - - + +
85I LEU* 4.6 12.8 - - + -
97I GLY 4.8 2.1 - - - +
100I ALA* 5.0 1.6 - - + -
101I LEU* 3.5 26.4 - - + +
104I ILE* 3.5 16.4 - - + -
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Residues in contact with GLU 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G VAL* 4.0 19.2 - - + +
15I ARG* 2.9 48.4 + - - +
16I ILE* 3.5 17.9 - - - +
17I GLU 3.2 0.2 - - - -
18I ALA* 1.3 76.2 - - - +
20I SER* 1.3 59.4 + - - +
22I LYS* 3.3 2.9 + - - +
23I ALA* 2.9 28.6 + - - +
101I LEU* 3.8 22.1 - - + +
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Residues in contact with SER 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G HIS* 2.8 35.1 - - - -
2G CYS* 4.8 0.2 - - - -
6G CYS* 3.4 13.0 - - - -
8G VAL* 3.4 18.0 - - - +
16I ILE 3.3 2.7 + - - -
17I GLU 3.3 9.2 + - - -
19I GLU* 1.3 78.3 - - - +
21I VAL* 1.3 58.8 + - - +
23I ALA* 3.2 1.9 + - - +
24I ILE* 2.8 37.4 + - - +
47I ARG* 4.1 17.5 - - - -
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Residues in contact with VAL 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I GLU 3.2 14.3 + - - +
18I ALA* 3.3 15.5 - - - +
20I SER* 1.3 78.2 - - - +
22I LYS* 1.3 57.4 + - - +
24I ILE* 3.6 7.5 - - - +
25I GLN* 3.0 39.2 + - - +
44I LYS* 4.0 18.2 - - + +
47I ARG* 3.8 4.9 - - + +
48I ALA* 3.6 35.7 - - + +
85I LEU* 5.2 4.0 - - + -
88I ALA* 3.9 28.0 - - + -
97I GLY* 4.5 4.3 - - - -
100I ALA* 6.4 0.2 - - + -
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Residues in contact with LYS 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ALA 3.2 10.4 + - - +
19I GLU* 3.9 6.3 - - - +
20I SER 3.3 0.2 - - - -
21I VAL* 1.3 76.2 - - - +
23I ALA* 1.3 66.6 + - - +
25I GLN* 3.1 10.8 + - - +
26I GLU* 2.9 47.5 + - - +
94I PRO* 3.7 30.7 - - + +
97I GLY* 4.4 7.9 - - - -
98I GLN* 2.5 42.9 + - - +
101I LEU* 4.1 14.1 - - + -
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Residues in contact with ALA 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G CYS 3.6 22.4 - - - +
8G VAL* 3.9 11.9 - - + -
19I GLU 2.9 18.8 + - - +
20I SER* 3.2 5.1 + - - +
22I LYS* 1.3 76.6 - - - +
24I ILE* 1.3 56.9 + - - +
26I GLU* 3.4 15.8 + - - +
27I LYS* 3.1 34.3 + - - +
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Residues in contact with ILE 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G CYS* 4.2 8.7 - - - -
4G LEU* 3.7 15.9 - - + -
6G CYS* 4.0 9.2 - - + -
20I SER 2.8 26.6 + - - +
21I VAL 3.6 4.5 - - - +
23I ALA* 1.3 75.0 - - - +
25I GLN* 1.3 59.6 + - - +
27I LYS* 3.1 7.2 + - - +
28I MET* 2.9 37.9 + - + +
40I ALA* 3.5 35.4 - - + +
43I ILE* 3.7 30.7 - - + -
44I LYS* 3.9 23.1 - - + +
47I ARG* 4.2 7.0 - - + -
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Residues in contact with GLN 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I VAL* 3.0 18.7 + - - +
22I LYS* 3.1 9.4 + - - +
24I ILE* 1.3 75.5 - - - +
26I GLU* 1.3 63.0 + - - +
28I MET* 3.4 14.1 + - - +
29I ALA* 3.4 10.9 + - - +
44I LYS* 3.5 13.2 - - + -
88I ALA* 3.2 12.5 + - - +
91I SER 2.8 24.1 + - - +
92I THR 3.6 21.8 - - - +
93I ASP 3.5 5.8 + - - -
94I PRO* 3.3 18.5 - - + +
96I THR* 2.8 23.7 + - - -
97I GLY* 3.0 28.6 + - - -
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Residues in contact with GLU 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I LYS* 2.9 40.1 + - - +
23I ALA* 3.6 16.7 - - - +
25I GLN* 1.3 78.0 - - - +
27I LYS* 1.3 62.3 + - + +
28I MET 3.6 0.3 + - - -
29I ALA* 3.7 11.5 + - - +
30I ALA* 3.9 10.0 + - - +
94I PRO* 3.9 23.4 - - + +
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Residues in contact with LYS 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G LEU* 4.5 6.5 - - + -
5G PRO* 3.7 17.7 - - - +
6G CYS* 3.4 34.1 - - - +
7G GLY* 4.5 2.5 - - - +
9007G SO4 5.9 0.4 - - - -
23I ALA* 3.1 20.1 + - - +
24I ILE* 3.1 5.4 + - - +
26I GLU* 1.3 76.2 - - + +
28I MET* 1.3 65.7 + - - +
30I ALA* 3.2 15.0 + - - +
31I ASN* 3.4 10.4 + - - +
36I PHE* 3.5 23.6 - - + -
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Residues in contact with MET 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I ILE* 2.9 26.9 + - - +
25I GLN* 3.6 7.6 - - - +
26I GLU 3.3 0.2 - - - -
27I LYS* 1.3 77.5 - - - +
29I ALA* 1.3 62.1 + - - +
30I ALA 3.0 1.4 + - - -
31I ASN 3.4 6.4 + - - -
32I ASP* 4.4 1.0 + - - +
36I PHE* 3.8 3.8 - - + -
37I GLN* 2.9 56.1 + - - +
40I ALA* 3.5 24.7 - - + -
41I THR* 3.4 25.6 - - - +
44I LYS* 3.8 26.9 - - - -
92I THR* 4.1 17.3 - - + -
35K HIS* 3.8 12.3 - - + +
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Residues in contact with ALA 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I GLN 3.4 9.1 + - - +
26I GLU* 3.9 10.1 - - - +
27I LYS 3.3 0.6 - - - -
28I MET* 1.3 78.1 - - - +
30I ALA* 1.3 58.5 + - - +
32I ASP* 5.5 1.3 + - - +
92I THR* 5.3 5.6 + - - +
94I PRO* 5.6 5.2 - - + -
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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