Contacts of the helix formed by residues 11 - 30 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ASP* 1.3 87.3 - - - +
12G ALA* 1.3 62.0 + - - +
13G GLN 3.1 0.7 - - - -
14G ALA* 3.1 10.3 + - + +
15G ARG* 2.9 22.5 + - - +
55G LEU* 5.7 0.4 - - + -
58G LEU* 3.7 27.1 - - + -
104G ILE* 4.4 7.6 - - + +
107G ILE* 4.9 2.5 - - + +
108G ASP* 3.4 31.9 - - + +
111G PHE* 3.4 48.0 - - + -
112G TRP* 4.9 0.2 - - - +
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Residues in contact with ALA 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ASP* 2.7 31.3 + - - +
11G PRO* 1.3 73.5 - - - +
13G GLN* 1.3 56.2 + - - +
15G ARG* 3.6 35.3 - - - +
16G ILE* 2.9 41.7 + - + +
108G ASP* 4.7 0.2 + - - -
12I ALA* 5.9 2.7 - - + -
16I ILE* 4.4 10.1 - - + -
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Residues in contact with GLN 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G HIS* 3.7 33.9 + - - +
10G ASP 3.0 19.3 + - - +
12G ALA* 1.3 80.6 - - - +
14G ALA* 1.3 61.0 + - - +
16G ILE* 3.6 7.1 + - - +
17G GLU* 3.4 18.0 + - - +
54G HIS* 3.5 44.6 + - + +
13I GLN* 5.4 7.2 + - - +
16I ILE* 4.0 28.5 - - + +
17I GLU* 3.2 27.3 + - - +
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Residues in contact with ALA 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G PRO* 3.1 11.7 + - + +
13G GLN* 1.3 78.6 - - - +
15G ARG* 1.3 65.5 + - - +
17G GLU* 3.2 4.3 + - - +
18G ALA* 3.0 23.0 + - - +
51G ALA* 4.0 8.5 - - - +
54G HIS* 3.9 22.1 - - + +
55G LEU* 3.7 34.3 - - + -
58G LEU* 5.6 0.4 - - + -
104G ILE* 4.2 10.3 - - + -
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Residues in contact with ARG 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ASP* 5.3 0.2 + - - -
11G PRO 2.9 12.5 + - - +
12G ALA* 3.2 38.3 + - - +
14G ALA* 1.3 77.1 - - - +
16G ILE* 1.3 68.1 + - - +
18G ALA* 3.2 2.4 + - - +
19G GLU* 2.8 61.1 + - + +
101G LEU* 4.2 9.6 - - + +
104G ILE* 4.2 21.9 - - + +
108G ASP* 4.9 12.5 + - - -
10I ASP* 4.8 8.3 + - - -
12I ALA* 6.1 0.8 - - - +
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Residues in contact with ILE 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G ALA* 2.9 28.6 + - + +
13G GLN* 3.9 5.6 - - - +
15G ARG* 1.3 87.0 - - - +
17G GLU* 1.3 63.4 + - - +
19G GLU* 3.4 13.9 + - - +
20G SER* 3.3 19.8 + - - -
1I HIS* 4.1 10.3 - - + -
8I VAL* 4.0 11.0 - - + +
10I ASP* 3.9 33.0 - - + +
12I ALA* 4.2 11.0 - - + -
13I GLN* 3.8 44.4 - - + +
16I ILE* 5.8 1.8 - - + -
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Residues in contact with GLU 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G GLN 3.4 12.7 + - - +
14G ALA 3.2 7.4 + - - +
16G ILE* 1.3 74.1 - - - +
18G ALA* 1.3 66.1 + - - +
20G SER* 3.1 7.1 + - - -
21G VAL* 3.1 22.9 + - - +
47G ARG* 3.1 47.1 + - - +
50G LEU* 3.9 21.0 - - + +
51G ALA* 3.8 6.3 - - + -
54G HIS* 4.0 13.1 + - + -
1I HIS* 3.0 24.2 + - - -
13I GLN* 3.0 24.5 + - - -
7009I THJ 4.2 4.7 - - - -
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Residues in contact with ALA 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ALA 3.0 16.6 + - - +
15G ARG 3.7 0.4 - - - +
17G GLU* 1.3 73.3 - - - +
19G GLU* 1.3 65.6 + - - +
21G VAL* 3.2 13.3 + - - +
22G LYS* 3.1 21.0 + - - +
51G ALA* 4.1 4.0 - - + +
85G LEU* 4.2 15.0 - - + -
97G GLY 4.8 1.8 - - - +
100G ALA* 5.0 2.7 - - + -
101G LEU* 3.7 18.6 - - + +
104G ILE* 3.5 24.5 - - + -
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Residues in contact with GLU 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G ARG* 2.8 49.9 + - - +
16G ILE* 3.7 13.5 - - - +
17G GLU 3.2 0.2 - - - -
18G ALA* 1.3 73.8 - - - +
20G SER* 1.3 65.5 + - - +
22G LYS* 3.3 2.6 + - - +
23G ALA* 2.9 25.1 + - - +
101G LEU* 3.6 25.8 - - + +
8I VAL* 3.9 17.3 - - + +
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Residues in contact with SER 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ILE 3.3 2.2 + - - -
17G GLU 3.1 11.1 + - - -
19G GLU* 1.3 79.4 - - - +
21G VAL* 1.3 64.7 + - - +
23G ALA* 3.2 1.3 + - - +
24G ILE* 2.8 30.8 + - - +
47G ARG* 4.2 15.7 - - - -
1I HIS* 2.8 35.0 - - - -
2I CYS* 5.0 0.2 - - - -
6I CYS* 3.2 20.1 - - - -
8I VAL* 3.4 12.4 - - - +
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Residues in contact with VAL 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G GLU 3.1 16.9 + - - +
18G ALA* 3.2 14.8 + - + +
20G SER* 1.3 76.6 - - - +
22G LYS* 1.3 63.2 + - - +
24G ILE* 3.3 10.0 + - - +
25G GLN* 3.1 35.6 + - - +
44G LYS* 4.0 14.0 - - + +
47G ARG* 3.9 4.9 - - + -
48G ALA* 3.5 39.3 - - + +
85G LEU* 5.0 4.9 - - + -
88G ALA* 3.8 28.7 - - + -
97G GLY* 4.5 4.5 - - - -
100G ALA* 6.3 0.2 - - + -
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Residues in contact with LYS 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ALA 3.1 12.8 + - - +
19G GLU 3.8 5.6 - - - +
20G SER 3.2 0.2 - - - -
21G VAL* 1.3 76.2 - - - +
23G ALA* 1.3 64.3 + - - +
25G GLN* 3.0 13.5 + - - +
26G GLU* 2.8 53.1 + - - +
94G PRO* 3.7 21.5 - - + +
97G GLY* 4.3 5.4 - - - -
98G GLN* 2.8 53.7 + - - +
101G LEU* 3.8 13.9 - - + -
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Residues in contact with ALA 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G GLU 2.9 17.0 + - - +
20G SER 3.7 3.6 - - - +
22G LYS* 1.3 77.0 - - - +
24G ILE* 1.3 61.2 + - - +
26G GLU* 3.5 17.6 + - - +
27G LYS* 3.2 28.4 + - - +
6I CYS 3.6 21.8 - - - +
8I VAL* 3.9 13.2 - - + -
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Residues in contact with ILE 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G SER 2.8 30.7 + - - +
21G VAL* 3.5 5.4 - - - +
22G LYS 3.1 0.2 - - - -
23G ALA* 1.3 77.1 - - - +
25G GLN* 1.3 59.0 + - - +
27G LYS* 3.2 6.2 + - - +
28G MET* 2.9 35.4 + - - +
40G ALA* 3.5 27.6 - - + +
43G ILE* 3.8 22.4 - - + -
44G LYS* 3.8 28.9 - - + -
47G ARG* 4.1 8.5 - - + -
2I CYS* 4.2 5.4 - - - -
4I LEU* 3.7 22.0 - - + -
6I CYS* 3.9 14.8 - - + -
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Residues in contact with GLN 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G VAL* 3.1 15.6 + - - +
22G LYS* 3.0 10.4 + - - +
24G ILE* 1.3 75.4 - - - +
26G GLU* 1.3 63.0 + - - +
28G MET* 3.1 10.2 + - - +
29G ALA* 3.0 21.3 + - - +
44G LYS* 3.5 15.2 - - + +
88G ALA* 3.3 15.6 + - - +
91G SER 2.9 23.3 + - - +
92G THR 3.3 21.6 - - - +
93G ASP 3.3 8.3 + - - +
94G PRO* 3.4 12.2 - - + +
96G THR* 2.9 20.0 + - - -
97G GLY* 3.1 27.1 + - - -
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Residues in contact with GLU 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G LYS* 2.8 45.7 + - - +
23G ALA* 3.6 17.6 - - - +
25G GLN* 1.3 77.9 - - - +
27G LYS* 1.3 63.5 + - + +
29G ALA* 3.3 16.0 + - - +
30G ALA* 3.7 7.3 + - - +
94G PRO* 3.9 22.7 - - + +
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Residues in contact with LYS 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G ALA* 3.2 12.7 + - - +
24G ILE* 3.2 7.9 + - - +
26G GLU* 1.3 77.8 - - + +
28G MET* 1.3 61.6 + - - +
30G ALA* 3.1 14.1 + - - +
31G ASN* 3.4 17.3 + - - +
36G PHE* 3.9 19.1 - - + -
4I LEU* 4.3 11.4 - - + -
5I PRO* 3.2 24.4 + - - +
6I CYS* 3.1 29.9 + - - -
7I GLY* 5.0 2.8 - - - +
9009I SO4 5.9 0.2 + - - -
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Residues in contact with MET 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G ILE* 2.9 22.0 + - - +
25G GLN* 3.1 12.8 + - - +
27G LYS* 1.3 76.7 - - - +
29G ALA* 1.3 61.4 + - - +
30G ALA 3.4 0.2 + - - -
31G ASN 3.7 3.7 + - - -
32G ASP* 4.4 4.2 - - - +
36G PHE* 4.2 4.5 - - + -
37G GLN* 3.2 54.2 + - - +
40G ALA* 3.6 25.1 - - + -
41G THR* 3.5 25.4 - - - +
44G LYS* 3.8 25.8 - - - -
92G THR* 3.7 29.1 - - + -
35J HIS* 3.7 1.1 - - + +
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Residues in contact with ALA 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G GLN 3.0 11.5 + - - +
26G GLU* 3.5 13.9 - - - +
27G LYS 3.1 0.4 - - - -
28G MET* 1.3 78.2 - - - +
30G ALA* 1.3 58.7 + - + +
31G ASN 3.7 0.2 - - - -
32G ASP* 5.5 2.0 - - - +
92G THR* 5.2 2.9 - - - +
94G PRO* 4.9 12.1 - - + -
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Residues in contact with ALA 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G GLU 3.7 6.0 + - - +
27G LYS* 3.1 8.4 + - - +
29G ALA* 1.3 80.7 - - - +
31G ASN* 1.3 61.0 + - - +
32G ASP 4.3 0.2 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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