Contacts of the helix formed by residues 5 - 21 (chain G) in PDB entry 4UN7
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 GLU 5 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6G GLU* 1.3 66.3 + - - +
7G VAL* 3.2 11.3 - - - +
8G SER* 3.3 28.6 + - - +
9G GLY 3.4 7.1 + - - -
104G ARG* 3.4 34.0 - - - +
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Residues in contact with GLU 6 (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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5G GLU* 1.3 78.0 - - - +
7G VAL* 1.3 59.9 + - + +
9G GLY* 3.6 1.4 + - - -
10G ILE* 3.1 60.1 + - + +
58G PHE* 4.0 18.3 - - - -
104G ARG* 5.5 0.4 - - - +
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Residues in contact with VAL 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G GLU 3.8 6.3 - - - +
6G GLU* 1.3 76.4 - - + +
8G SER* 1.3 60.6 + - - +
10G ILE* 3.5 2.4 + - - +
11G SER* 2.8 33.4 + - - +
58G PHE* 3.8 24.0 - - + -
59G LEU* 4.2 14.2 - - + +
62G GLU* 3.5 35.9 - - + +
63G LEU* 5.2 5.2 - - + -
90G TYR* 4.0 16.6 - - + +
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Residues in contact with SER 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G GLU* 3.3 24.5 + - - +
7G VAL* 1.3 79.6 - - - +
9G GLY* 1.3 57.6 + - - +
11G SER* 3.3 8.6 - - - -
12G ALA* 2.9 29.3 + - - +
90G TYR* 4.9 2.2 - - - -
94G MET* 3.8 5.0 - - - +
102G ASN* 5.3 4.0 + - - -
104G ARG* 5.1 1.7 - - - -
105G GLU* 3.5 27.6 + - - +
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Residues in contact with GLY 9 (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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5G GLU 3.4 10.7 + - - -
6G GLU* 4.0 2.5 - - - -
7G VAL 3.3 0.8 - - - -
8G SER* 1.3 78.3 + - - +
10G ILE* 1.3 66.1 + - - +
12G ALA* 3.3 1.9 + - - -
13G TYR* 3.1 19.8 + - - +
104G ARG* 4.3 18.8 - - - -
105G GLU* 4.8 1.8 - - - +
108G ALA* 3.2 19.4 - - - +
181G HIS* 4.4 5.5 - - - -
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Residues in contact with ILE 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLU* 3.1 45.9 + - + +
7G VAL* 3.9 4.0 - - - +
9G GLY* 1.3 75.5 - - - +
11G SER* 1.3 64.6 + - - +
13G TYR* 3.3 7.4 + - - +
14G LEU* 2.9 40.5 + - + +
55G LEU* 4.1 42.2 - - + +
58G PHE* 3.7 22.2 - - + -
59G LEU* 5.2 3.6 - - + -
181G HIS* 5.1 9.6 - - + +
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Residues in contact with SER 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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7G VAL 2.8 21.9 + - - -
8G SER* 3.3 7.9 - - - -
9G GLY 3.2 0.2 - - - -
10G ILE* 1.3 77.9 - - - +
12G ALA* 1.3 57.8 + - - +
14G LEU* 3.2 8.4 + - - +
15G LEU* 2.9 27.5 + - - +
59G LEU* 3.6 12.4 - - - +
90G TYR* 2.6 37.7 + - - -
91G PHE* 3.7 8.1 - - - -
94G MET* 3.8 17.9 - - - -
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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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8G SER 2.9 18.7 + - - +
9G GLY 3.7 4.7 - - - +
10G ILE 3.3 0.4 - - - -
11G SER* 1.3 71.2 - - - +
13G TYR* 1.3 66.7 + - - +
15G LEU* 3.2 4.2 + - - -
16G GLY 3.0 18.5 + - - -
94G MET* 3.7 15.9 - - + +
101G PHE* 4.0 7.6 - - + -
105G GLU* 3.5 33.9 - - - +
108G ALA* 4.0 0.2 - - + -
109G PHE* 3.4 17.0 - - - +
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Residues in contact with TYR 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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9G GLY 3.1 13.7 + - - +
10G ILE* 3.6 9.2 - - - +
11G SER 3.3 0.2 - - - -
12G ALA* 1.3 77.4 - - - +
14G LEU* 1.3 67.0 + - + +
16G GLY* 3.3 4.0 + - - -
17G LEU* 3.1 41.6 + - + +
51G HIS* 2.6 37.7 + + - -
55G LEU* 3.9 22.2 - - + -
108G ALA* 3.6 18.1 - - + +
111G LYS* 4.0 25.1 - - + -
112G GLY* 3.6 33.3 - - - -
115G VAL* 4.0 16.7 - - + +
181G HIS* 4.3 14.1 - + + -
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Residues in contact with LEU 14 (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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10G ILE* 2.9 33.1 + - + +
11G SER 3.2 6.9 + - - +
13G TYR* 1.3 78.5 - - + +
15G LEU* 1.3 60.5 + - - +
17G LEU* 3.1 13.8 + - + +
18G ILE* 2.9 36.7 + - + +
40G ILE* 4.0 6.9 - - + +
52G ILE* 4.4 22.2 - - + -
55G LEU* 4.1 24.9 - - + +
56G MET* 4.1 18.8 - - + +
59G LEU* 3.8 27.1 - - + -
91G PHE* 4.1 9.6 - - + -
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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
----------------------------------------------------------
11G SER 2.9 17.4 + - - +
12G ALA* 3.2 7.8 + - - +
14G LEU* 1.3 78.4 - - - +
16G GLY* 1.3 57.3 + - - +
18G ILE* 3.3 13.4 + - + -
19G ILE* 2.9 42.4 + - + +
24G LEU* 4.8 4.0 - - + -
91G PHE* 4.0 33.9 - - + +
94G MET* 4.5 6.3 - - + -
95G LEU* 4.1 29.2 - - + +
98G ILE* 5.1 0.9 - - + -
101G PHE* 4.1 22.0 - - + -
109G PHE* 3.9 18.6 - - + -
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Residues in contact with GLY 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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12G ALA 3.0 12.3 + - - -
13G TYR 3.3 4.9 + - - -
14G LEU 3.2 0.2 - - - -
15G LEU* 1.3 74.5 - - - +
17G LEU* 1.3 65.5 + - - +
19G ILE* 4.0 0.4 - - - -
20G GLY* 3.0 21.7 + - - -
109G PHE* 3.7 17.2 - - - -
112G GLY 3.8 6.9 - - - +
113G LEU* 3.7 24.4 - - - +
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Residues in contact with LEU 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 TYR* 3.1 33.1 + - + +
14G LEU* 3.1 6.9 + - + +
16G GLY* 1.3 73.8 - - - +
18G ILE* 1.3 54.1 + - - +
21G ASP* 2.6 40.0 + - + +
22G GLY 3.7 0.7 + - - -
40G ILE* 3.6 21.9 - - + +
42G GLN* 5.7 3.8 - - - +
51G HIS* 5.4 0.2 - - + -
52G ILE* 3.6 46.7 - - + -
112G GLY* 3.4 26.7 - - - +
115G VAL* 3.9 23.1 - - + -
116G ALA* 4.4 8.5 - - + +
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Residues in contact with ILE 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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14G LEU 2.9 20.6 + - - +
15G LEU* 3.5 9.4 - - + +
17G LEU* 1.3 76.6 - - - +
19G ILE* 1.3 62.0 + - + +
22G GLY 2.8 34.0 + - - +
23G GLY* 3.6 30.2 - - - +
24G LEU* 4.0 13.7 - - + -
38G VAL* 3.5 25.8 - - + -
39G VAL 3.8 3.4 - - - +
40G ILE* 3.5 26.9 - - + -
56G MET* 4.8 1.1 - - + -
91G PHE* 3.8 33.0 - - + -
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Residues in contact with ILE 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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15G LEU* 2.9 22.7 + - + +
16G GLY 4.2 1.8 - - - +
18G ILE* 1.3 81.3 - - + +
20G GLY* 1.3 62.0 + - - +
22G GLY 4.7 4.3 - - - +
23G GLY* 5.8 0.7 - - - -
24G LEU* 6.2 0.9 - - + -
95G LEU* 3.5 42.0 - - + -
109G PHE* 4.0 25.1 - - + -
113G LEU* 4.3 8.5 - - + -
117G GLU* 4.2 4.3 - - - +
129G ASN* 4.3 7.9 + - - +
134G LEU* 3.6 30.3 - - + -
15H G 5.1 2.4 - - - +
15I C 4.8 1.6 + - - -
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Residues in contact with GLY 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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16G GLY 3.0 15.9 + - - -
19G ILE* 1.3 82.0 - - - +
21G ASP* 1.3 65.3 + - - +
113G LEU* 4.1 3.1 - - - +
116G ALA* 3.8 4.3 - - - -
117G GLU* 3.1 34.9 - - - +
15H G 3.0 22.1 + - - +
15I C 4.1 0.5 + - - -
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Residues in contact with ASP 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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17G LEU* 2.6 19.5 + - - +
20G GLY* 1.3 78.2 - - - +
22G GLY* 1.3 55.6 + - - +
40G ILE* 4.6 2.2 - - + -
41G THR* 2.4 50.1 + - - +
42G GLN* 2.7 25.4 + - - +
116G ALA* 3.3 15.5 - - + +
1182G ZN 2.7 34.6 - - - -
14H A 3.3 15.1 - - - +
15H G 3.5 9.9 - - - +
16I C 3.3 2.3 + - - -
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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