Contacts of the helix formed by residues 6 - 19 (chain G) in PDB entry 4NL3
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 GLN 6 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2G LYS* 5.6 0.6 - - - +
3G GLN* 2.5 44.2 + - + +
4G GLY 3.3 1.3 + - - +
5G GLY* 1.3 76.6 - - - +
7G GLY* 1.3 62.4 + - - +
8G LEU 3.5 1.1 - - - -
9G GLN* 3.6 18.3 + - - +
10G ASP* 3.4 36.2 + - - +
42G ASN* 3.4 14.5 + - - +
58G LYS* 5.2 0.2 + - - -
41H ASP* 3.4 9.9 - - - +
43H PHE* 4.2 12.4 - - + -
21R U 2.7 44.5 + - - +
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Residues in contact with GLY 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G LYS* 3.6 29.5 - - - +
5G GLY* 3.5 4.8 - - - -
6G GLN* 1.3 74.3 - - - +
8G LEU* 1.3 59.5 + - - +
10G ASP* 3.4 2.7 + - - +
11G TYR* 2.9 34.4 + - - +
41H ASP* 4.2 1.0 + - - +
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Residues in contact with LEU 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLN 3.5 0.2 - - - -
7G GLY* 1.3 75.8 - - - +
9G GLN* 1.3 56.5 + - - +
11G TYR* 4.0 6.8 - - + +
12G TYR* 3.1 30.5 + - + +
72G LEU* 4.4 13.5 - - + -
39H SER* 3.7 30.5 - - - +
40H PHE* 4.3 12.6 - - - +
41H ASP* 3.9 16.9 + - + +
44H THR* 3.2 26.5 - - - +
46H LEU* 4.3 24.2 - - + +
55H LEU* 3.9 16.6 - - + -
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Residues in contact with GLN 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLN* 3.6 23.8 + - - +
7G GLY 3.2 0.4 - - - -
8G LEU* 1.3 76.7 - - - +
10G ASP* 1.3 66.6 + - - +
12G TYR* 4.0 2.8 - - - +
13G LEU* 3.1 37.0 + - + +
58G LYS* 2.7 32.4 + - - -
41H ASP* 3.1 16.8 + - - +
43H PHE* 3.9 8.6 - - - +
44H THR* 3.5 26.5 - - + +
55H LEU* 5.0 2.9 - - + -
57H PHE* 3.4 13.2 - - + -
21R U 2.7 24.3 + - - +
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Residues in contact with ASP 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLN* 3.4 38.3 + - - +
7G GLY* 3.4 3.6 + - - +
9G GLN* 1.3 85.1 + - - +
11G TYR* 1.3 57.5 + - - +
14G ASN* 3.1 28.1 + - - +
40G PHE* 3.5 25.6 - - + -
42G ASN* 5.2 2.9 - - - +
58G LYS* 4.8 3.3 + - - -
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Residues in contact with TYR 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G GLY 2.9 19.8 + - - +
8G LEU* 4.0 8.1 - - + +
10G ASP* 1.3 75.8 - - - +
12G TYR* 1.3 68.6 + - + +
14G ASN* 3.1 7.9 + - + +
15G GLN* 3.0 59.5 + - + +
70G VAL* 4.3 4.3 - - + -
71G ALA* 2.6 31.8 + - - +
72G LEU* 4.2 18.2 - - + -
73G ASN* 3.3 29.8 + - - -
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Residues in contact with TYR 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G LEU* 3.1 21.0 + - + +
9G GLN 4.0 0.7 - - - +
11G TYR* 1.3 83.7 - + + +
13G LEU* 1.3 63.6 + - - +
14G ASN 3.3 0.2 + - - -
15G GLN* 3.4 4.1 + - - +
16G LEU* 3.3 52.8 + - + +
64G PHE* 5.1 0.9 - - + -
66G PRO* 3.3 19.5 - - + +
70G VAL* 3.9 20.2 - - + +
72G LEU* 5.1 3.8 - - + -
46H LEU* 3.5 34.2 - - + +
53H GLN* 2.5 44.1 + - - +
55H LEU* 3.5 38.8 - - + -
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Residues in contact with LEU 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G GLN* 3.1 36.0 + - + +
12G TYR* 1.3 77.3 - - - +
14G ASN* 1.3 62.2 + - - +
16G LEU* 4.0 11.5 - - + +
17G ARG* 3.5 16.8 + - - +
37G VAL* 3.8 12.2 - - + +
40G PHE* 3.3 44.0 - - + -
45G VAL* 4.3 9.6 - - + -
58G LYS* 4.2 17.3 - - - +
64G PHE* 3.8 39.9 - - + -
55H LEU* 4.5 7.4 - - + -
57H PHE* 4.9 2.2 - - + -
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Residues in contact with ASN 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 ASP 3.1 20.7 + - - +
11G TYR* 3.3 10.8 - - - +
12G TYR 3.1 0.4 - - - -
13G LEU* 1.3 76.6 - - - +
15G GLN* 1.3 60.5 + - - +
17G ARG* 2.2 44.6 + - - +
18G LYS* 2.8 52.6 + - - +
40G PHE* 3.6 9.0 - - + -
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Residues in contact with GLN 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G TYR* 3.0 53.8 + - + +
12G TYR 4.0 1.1 - - - +
14G ASN* 1.3 76.8 - - - +
16G LEU* 1.3 59.0 + - - +
18G LYS* 4.0 29.9 - - - +
19G GLU* 2.5 62.6 + - + +
21G ILE* 5.0 0.9 - - - -
70G VAL* 3.7 25.8 - - + +
71G ALA* 6.1 1.4 - - - +
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Residues in contact with LEU 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G TYR* 3.3 36.7 + - + +
13G LEU* 4.0 7.9 - - + +
15G GLN* 1.3 78.1 - - - +
17G ARG* 1.3 59.8 + - - +
20G LYS* 3.4 3.3 + - - -
21G ILE* 3.2 54.4 + - + +
23G ALA* 4.7 7.9 - - + -
36G ARG* 5.5 0.3 - - - +
37G VAL* 3.9 25.4 + - + +
64G PHE* 4.3 24.2 - - + -
66G PRO* 3.9 17.5 - - + -
70G VAL* 3.7 21.3 - - + -
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Residues in contact with ARG 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G LEU 3.5 10.4 + - - +
14G ASN* 2.2 55.2 + - - +
15G GLN 3.0 0.8 - - - -
16G LEU* 1.3 78.9 - - - +
18G LYS* 1.3 83.5 + - - +
20G LYS* 3.6 19.9 + - - +
37G VAL* 3.3 30.9 - - + +
38G VAL* 3.1 23.8 + - - +
39G SER* 4.4 7.0 - - - +
40G PHE* 4.8 7.1 - - - -
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Residues in contact with LYS 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ASN* 2.8 41.6 + - - +
15G GLN* 3.7 21.9 - - - +
17G ARG* 1.3 100.5 - - - +
19G GLU* 1.3 65.8 + - + +
20G LYS* 3.1 10.4 + - - +
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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 GLN* 2.5 45.0 + - + +
18G LYS* 1.3 74.9 - - + +
20G LYS* 1.3 68.5 + - - +
21G ILE* 3.0 23.8 + - + +
68G LYS* 6.0 2.1 - - + +
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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