Contacts of the helix formed by residues 9 - 24 (chain G) in PDB entry 5UKM
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 ILE 9 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B GLU* 3.5 43.9 - - + +
4B LEU* 4.1 26.9 - - + +
7B LEU* 3.9 4.8 - - + +
8G SER* 1.3 78.0 - - - +
10G ALA* 1.3 65.1 + - - +
11G GLN 3.1 2.1 + - - -
12G ALA 3.8 0.3 + - - -
13G ARG* 3.6 21.7 + - - +
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Residues in contact with ALA 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G SER* 5.2 1.3 - - - -
9G ILE* 1.3 81.1 - - - +
11G GLN* 1.3 58.3 + - - +
13G ARG* 3.8 24.7 + - - +
14G LYS* 3.5 18.0 + - - +
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Residues in contact with GLN 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G SER* 3.6 29.5 + - - +
9G ILE 3.1 1.4 - - - -
10G ALA* 1.3 76.8 - - + +
12G ALA* 1.3 59.0 + - - +
13G ARG 3.2 4.9 - - - -
14G LYS* 3.3 13.4 + - + +
15G LEU* 3.3 19.2 + - - +
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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
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4B LEU* 4.0 25.1 - - + -
7B LEU* 3.9 24.9 - - + +
8B ARG* 5.0 7.4 - - + +
8G SER 3.5 5.2 + - - +
9G ILE 3.8 0.4 + - - +
10G ALA 3.8 0.2 - - - -
11G GLN* 1.3 75.4 - - - +
13G ARG* 1.3 61.1 + - - +
15G LEU* 3.8 17.3 - - + +
16G VAL* 3.6 23.9 + - - +
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Residues in contact with ARG 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B GLU* 4.1 17.4 + - - -
7B LEU* 3.6 28.2 - - + +
9G ILE 3.6 12.9 + - - +
10G ALA* 3.8 21.3 + - - +
11G GLN 3.2 0.6 - - - -
12G ALA* 1.3 77.7 - - - +
14G LYS* 1.3 62.6 + - - +
15G LEU 3.4 0.2 - - - -
16G VAL* 3.5 4.1 + - + +
17G GLU* 3.3 32.0 + - + +
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Residues in contact with LYS 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B THR* 4.4 15.4 + - - -
10G ALA 3.5 11.5 + - - +
11G GLN* 3.3 17.8 + - + +
13G ARG* 1.3 78.1 - - - +
15G LEU* 1.3 63.4 + - - +
17G GLU* 3.6 6.2 + - + +
18G GLN* 3.1 23.7 + - - +
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Residues in contact with LEU 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 4.0 22.4 - - + -
15B LYS* 5.3 9.4 - - - +
11G GLN 3.3 10.3 + - - +
12G ALA* 3.8 18.4 - - + +
13G ARG 3.4 0.2 - - - -
14G LYS* 1.3 76.2 - - - +
16G VAL* 1.3 59.4 + - - +
18G GLN* 3.5 11.2 - - + +
19G LEU* 3.0 44.9 + - + +
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Residues in contact with VAL 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 4.0 24.7 - - + +
10B GLU* 3.7 35.7 - - + +
11B ALA* 4.5 7.0 - - + +
14B LEU* 3.7 21.7 - - + +
12G ALA 3.6 14.7 + - - +
13G ARG* 3.5 10.2 + - + +
14G LYS 3.3 1.0 - - - -
15G LEU* 1.3 74.7 - - - +
17G GLU* 1.3 64.5 + - + +
19G LEU* 2.9 21.4 + - - +
20G LYS* 3.0 23.7 + - - +
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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
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13G ARG* 3.3 26.3 + - + +
14G LYS* 4.1 5.8 - - + +
15G LEU 3.6 0.2 - - - -
16G VAL* 1.3 78.2 - - + +
18G GLN* 1.3 60.2 + - - +
20G LYS* 3.4 47.5 + - - +
21G MET* 3.7 12.3 + - - +
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Residues in contact with GLN 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B MET* 5.3 4.2 - - - +
218B CYS* 3.1 42.9 + - - +
14G LYS* 3.1 19.0 + - + +
15G LEU* 3.5 13.0 - - + +
16G VAL 3.1 0.4 - - - -
17G GLU* 1.3 74.4 - - - +
19G LEU* 1.3 63.0 + - + +
20G LYS 3.2 0.2 - - - -
21G MET* 2.9 29.7 + - - +
22G GLU* 2.8 44.0 + - - +
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Residues in contact with LEU 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ALA* 4.1 30.3 - - + +
14B LEU* 4.1 21.2 - - + +
15B LYS* 4.6 18.6 - - + +
18B ILE* 4.0 24.0 - - + +
15G LEU* 3.0 42.9 + - + +
16G VAL* 2.9 11.2 + - - +
18G GLN* 1.3 72.5 - - + +
20G LYS* 1.3 56.2 + - - +
22G GLU* 3.3 19.9 + - - +
23G ALA* 3.0 29.6 + - - +
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Residues in contact with LYS 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU* 4.9 8.0 + - - -
14B LEU* 4.1 17.0 - - + +
16G VAL* 3.0 26.1 + - + +
17G GLU* 3.4 44.0 + - - +
19G LEU* 1.3 75.4 - - - +
21G MET* 1.3 62.0 + - + +
23G ALA* 3.3 2.9 + - - +
24G ASN* 3.2 36.5 + - - +
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Residues in contact with MET 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B MET* 3.7 38.4 - - + -
218B CYS 5.2 4.5 - - - +
219B ARG* 4.4 6.1 - - - +
17G GLU 3.7 12.3 + - - +
18G GLN* 2.9 19.1 + - - +
20G LYS* 1.3 81.4 - - + +
22G GLU* 1.3 60.8 + - - +
23G ALA 3.4 0.3 + - - -
24G ASN* 3.7 17.8 + - - +
25G ILE* 3.9 7.1 - - - +
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Residues in contact with GLU 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 4.1 13.5 - - + +
22B ARG* 5.2 3.2 + - - +
209B LYS* 4.9 1.6 + - - -
218B CYS* 4.3 0.2 - - - -
219B ARG 3.7 19.4 - - - +
220B GLN* 4.2 9.5 - - - +
221B THR* 2.9 39.5 + - - +
258B ASP* 5.1 0.5 - - - +
18G GLN* 2.8 41.5 + - - +
19G LEU* 3.3 25.3 + - - +
21G MET* 1.3 77.3 - - - +
23G ALA* 1.3 60.6 + - - +
25G ILE* 3.6 12.6 - - - +
27G ARG* 3.5 15.2 + - - -
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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
----------------------------------------------------------
14B LEU* 4.9 4.5 - - + -
17B GLN* 4.0 27.1 - - + +
18B ILE* 3.9 20.4 - - + -
19G LEU 3.0 15.7 + - - +
20G LYS* 3.8 6.5 - - - +
21G MET 3.2 0.2 - - - -
22G GLU* 1.3 75.3 - - - +
24G ASN* 1.3 62.6 + - - +
25G ILE 2.9 9.8 + - - +
27G ARG* 3.1 20.4 + - - +
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Residues in contact with ASN 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLN* 5.6 2.8 - - - +
20G LYS* 3.2 30.7 + - - +
21G MET* 3.7 6.4 + - - +
22G GLU 3.7 0.2 - - - -
23G ALA* 1.3 77.4 - - - +
25G ILE* 1.3 67.7 + - - +
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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