Contacts of the helix formed by residues 6 - 19 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K GLN* 4.5 23.3 + - + +
4K GLY 3.5 5.6 - - - +
5K GLY 1.4 86.9 - - - +
7K GLY* 1.3 62.2 + - - +
8K LEU 3.6 1.3 - - - -
9K GLN* 3.6 5.4 + - - +
10K ASP* 3.0 41.9 + - - +
42K ASN* 3.3 13.8 + - - +
58K LYS* 5.0 1.0 + - - -
41L ASP* 3.5 11.9 - - - +
43L PHE* 3.7 18.8 - - + -
32Z U 2.7 48.0 + - - +
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Residues in contact with GLY 7 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K GLY 4.7 2.0 - - - +
5K GLY* 3.6 5.8 - - - +
6K GLN* 1.3 79.6 - - - +
8K LEU* 1.3 63.0 + - - +
10K ASP* 4.1 1.7 - - - +
11K TYR* 3.2 25.3 + - - +
41L ASP* 4.0 3.6 + - - +
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Residues in contact with LEU 8 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K GLN 3.6 0.2 - - - -
7K GLY* 1.3 74.1 - - - +
9K GLN* 1.3 55.7 + - - +
11K TYR* 3.9 6.9 - - + +
12K TYR* 3.1 31.4 + - + +
72K LEU* 4.6 10.8 - - + -
39L SER* 3.7 32.5 - - - +
40L PHE* 4.2 3.6 - - - +
41L ASP* 3.7 18.9 + - + +
44L THR* 3.1 30.5 - - - +
46L LEU* 4.2 26.5 - - + +
55L LEU* 3.6 20.6 - - + -
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Residues in contact with GLN 9 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K GLN* 3.6 13.9 + - - -
7K GLY 3.3 0.2 - - - -
8K LEU* 1.3 75.5 - - - +
10K ASP* 1.3 69.9 + - - +
12K TYR* 4.5 3.1 - - - -
13K LEU* 3.2 37.2 + - + +
40K PHE* 5.1 0.4 - - + -
58K LYS* 2.4 35.2 + - - -
41L ASP* 3.0 17.5 + - - +
43L PHE* 4.0 12.3 - - - +
44L THR* 3.5 21.1 - - + +
55L LEU* 5.0 3.1 - - + -
57L PHE* 3.4 16.4 - - + -
32Z U 2.6 23.8 + - - +
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Residues in contact with ASP 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K GLN 4.1 10.0 - - - +
6K GLN* 3.0 48.2 + - - +
7K GLY* 4.1 2.2 - - - +
9K GLN* 1.3 83.5 + - - +
11K TYR* 1.3 61.1 + - - +
14K ASN* 3.2 22.3 + - - +
40K PHE* 3.8 17.3 - - + -
42K ASN* 5.6 0.9 - - - +
58K LYS* 5.5 0.7 + - - -
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Residues in contact with TYR 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K GLY 3.2 18.4 + - - +
8K LEU* 3.9 8.1 - - + +
10K ASP* 1.3 76.9 - - - +
12K TYR* 1.3 71.7 + + + +
14K ASN* 3.3 6.5 + - + +
15K GLN* 3.1 55.3 + - + +
18K LYS* 5.8 1.3 - - - -
70K VAL* 4.4 5.8 - - + -
71K ALA* 2.3 34.9 + - - +
72K LEU* 3.8 27.7 + - + -
73K ASN* 5.0 7.7 - - + +
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Residues in contact with TYR 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K LEU* 3.1 24.2 + - + +
9K GLN 3.5 1.5 + - - +
11K TYR* 1.3 84.8 - + + +
13K LEU* 1.3 62.7 + - - +
15K GLN* 3.3 5.7 + - - +
16K LEU* 3.1 47.8 + - + +
64K PHE* 4.9 2.2 - - + -
66K PRO* 3.2 26.1 - - + +
70K VAL* 3.8 18.1 - - + +
72K LEU* 6.1 2.5 - - + -
46L LEU* 3.7 32.3 - - + +
53L GLN* 3.1 33.1 + - - +
55L LEU* 3.5 38.4 + - + -
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Residues in contact with LEU 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K GLN* 3.2 33.0 + - + +
12K TYR* 1.3 79.1 - - - +
14K ASN* 1.3 61.5 + - - +
16K LEU* 3.6 13.6 + - + +
17K ARG* 3.2 21.3 + - - +
37K VAL* 3.7 14.5 - - + +
40K PHE* 3.5 42.8 - - + -
45K VAL* 4.3 10.5 - - + -
58K LYS* 4.3 9.2 - - - -
64K PHE* 3.8 39.5 - - + -
55L LEU* 4.4 9.2 - - + -
57L PHE* 4.9 2.9 - - + -
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Residues in contact with ASN 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K ASP 3.2 20.6 + - - +
11K TYR* 3.3 6.7 + - - +
12K TYR 3.1 0.4 - - - -
13K LEU* 1.3 78.0 - - - +
15K GLN* 1.3 54.7 + - + +
17K ARG* 2.5 35.5 + - - +
18K LYS* 2.6 66.5 + - - +
40K PHE* 3.6 13.6 - - + -
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Residues in contact with GLN 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K TYR* 3.1 54.5 + - + +
12K TYR 3.3 4.2 + - - +
14K ASN* 1.3 73.8 - - + +
16K LEU* 1.3 57.6 + - - +
18K LYS* 3.1 30.1 + - - +
19K GLU* 2.7 62.2 + - + +
21K ILE* 4.6 1.1 - - - -
70K VAL* 3.7 23.5 - - + +
71K ALA* 4.9 4.6 + - - +
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Residues in contact with LEU 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K TYR* 3.1 35.4 + - + +
13K LEU* 3.7 14.4 - - + +
15K GLN* 1.3 77.2 - - - +
17K ARG* 1.3 58.7 + - - +
20K LYS* 3.3 16.5 + - - -
21K ILE* 3.3 53.0 + - + +
23K ALA* 4.5 9.0 - - + -
37K VAL* 3.8 28.9 + - + +
64K PHE* 4.2 20.0 - - + -
66K PRO* 4.0 9.0 - - + -
70K VAL* 3.6 16.6 - - + -
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Residues in contact with ARG 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K LEU 3.2 13.9 + - - +
14K ASN* 2.5 41.2 + - - +
16K LEU* 1.3 76.9 - - - +
18K LYS* 1.3 92.4 + - - +
20K LYS* 3.4 10.7 + - - +
37K VAL* 3.5 22.4 - - + +
38K VAL* 3.2 29.9 + - - +
39K SER* 4.4 7.6 - - - +
40K PHE* 4.7 7.4 - - + -
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Residues in contact with LYS 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K TYR* 5.8 2.0 - - - -
14K ASN* 2.6 41.8 + - - +
15K GLN* 3.1 30.5 + - - +
17K ARG* 1.3 96.7 - - - +
19K GLU* 1.3 61.9 + - + +
20K LYS* 3.1 11.6 + - - +
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Residues in contact with GLU 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K GLN* 2.7 44.6 + - + +
18K LYS* 1.3 71.6 - - + +
20K LYS* 1.3 66.5 + - - +
21K ILE* 2.9 20.0 + - + +
68K LYS* 5.1 13.3 + - - +
70K VAL* 6.5 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
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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