Contacts of the helix formed by residues 6 - 19 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ASP* 3.5 12.1 - - - +
43D PHE* 4.5 7.7 - - + -
3H GLN* 3.4 46.0 + - + +
4H GLY 3.2 1.7 + - - +
5H GLY* 1.3 76.9 - - - +
7H GLY* 1.3 62.0 + - - +
8H LEU 3.5 0.9 - - - -
9H GLN* 4.2 7.4 + - - +
10H ASP* 3.2 46.9 + - - +
42H ASN* 3.2 23.7 + - - +
58H LYS* 5.5 0.3 + - - -
22R U 3.0 29.8 + - - +
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Residues in contact with GLY 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ASP* 4.2 1.2 - - - +
2H LYS* 4.9 16.3 - - - +
3H GLN 4.6 1.0 + - - -
5H GLY* 3.4 7.3 - - - +
6H GLN* 1.3 76.3 - - - +
8H LEU* 1.3 58.6 + - - +
10H ASP* 4.1 1.5 - - - +
11H TYR* 3.0 33.4 + - - +
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Residues in contact with LEU 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D SER* 3.8 32.3 - - - +
40D PHE* 4.2 4.0 - - - +
41D ASP* 3.7 19.2 + - + +
44D THR* 3.1 29.8 - - - +
46D LEU* 4.1 29.2 - - + +
55D LEU* 3.7 20.2 - - + -
7H GLY* 1.3 74.8 - - - +
9H GLN* 1.3 56.8 + - - +
11H TYR* 4.1 6.6 - - + +
12H TYR* 3.1 33.6 + - + +
72H LEU* 4.9 10.1 - - + -
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Residues in contact with GLN 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ASP* 3.0 17.6 + - - +
43D PHE* 3.6 24.2 - - - +
44D THR* 3.4 19.8 - - + +
55D LEU* 4.9 2.7 - - + -
57D PHE* 3.9 9.2 - - + -
6H GLN* 4.6 3.2 - - - +
7H GLY 3.3 0.2 - - - -
8H LEU* 1.3 75.4 - - - +
10H ASP* 1.3 71.0 + - - +
12H TYR* 4.4 3.6 - - - -
13H LEU* 2.9 43.4 + - + +
58H LYS* 2.3 40.5 + - - +
22R U 2.9 22.6 + - - +
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Residues in contact with ASP 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H GLN* 3.2 50.2 + - - +
7H GLY* 4.2 1.3 - - - +
9H GLN* 1.3 84.4 - - - +
11H TYR* 1.3 62.2 + - - +
14H ASN* 3.2 24.6 + - - +
40H PHE* 3.8 19.8 - - + -
42H ASN* 5.2 2.0 - - - +
58H LYS* 5.1 1.7 + - - -
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Residues in contact with TYR 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H GLY 3.0 20.2 + - - +
8H LEU* 4.1 7.6 - - + +
10H ASP* 1.3 77.5 - - - +
12H TYR* 1.3 68.6 + + + +
14H ASN* 3.4 3.7 + - - +
15H GLN* 3.0 62.0 + - + +
18H LYS* 6.2 0.2 - - - -
70H VAL* 4.2 6.5 - - + -
71H ALA* 2.2 36.6 + - - +
72H LEU* 3.9 28.2 - - + -
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Residues in contact with TYR 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D LEU* 3.5 33.3 - - + +
53D GLN* 3.1 34.7 + - - +
55D LEU* 3.4 39.1 + - + -
8H LEU* 3.1 23.3 + - + +
9H GLN 3.9 0.9 - - - +
11H TYR* 1.3 83.9 - + + +
13H LEU* 1.3 60.7 - - - +
15H GLN* 3.4 5.0 + - - +
16H LEU* 3.1 46.1 + - + +
64H PHE* 4.8 2.9 - - + -
66H PRO* 3.2 25.4 - - + +
70H VAL* 3.8 19.4 - - + +
72H LEU* 6.1 1.3 - - + -
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Residues in contact with LEU 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D LEU* 4.5 7.4 - - + -
57D PHE* 4.9 2.5 - - + -
9H GLN* 2.9 42.8 + - + +
12H TYR* 1.3 76.9 - - - +
14H ASN* 1.3 60.7 + - - +
16H LEU* 3.7 14.5 + - + +
17H ARG* 3.3 20.3 + - - +
37H VAL* 3.9 12.6 - - + +
40H PHE* 3.5 35.3 - - + -
45H VAL* 4.2 19.3 - - + -
58H LYS* 4.2 2.0 - - - +
64H PHE* 3.6 42.0 - - + -
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Residues in contact with ASN 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H ASP 3.2 20.7 + - - +
11H TYR* 3.7 4.7 - - + +
12H TYR 3.2 0.4 - - - -
13H LEU* 1.3 78.5 - - - +
15H GLN* 1.3 53.6 + - + +
17H ARG* 2.6 34.0 + - - +
18H LYS* 2.7 61.9 + - - +
40H PHE* 3.7 16.2 - - + -
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Residues in contact with GLN 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H TYR* 3.0 56.6 + - + +
12H TYR 3.4 2.0 + - - +
14H ASN* 1.3 74.3 - - + +
16H LEU* 1.3 59.7 + - - +
18H LYS* 3.0 32.0 + - - +
19H GLU* 2.9 59.4 + - + +
21H ILE* 4.3 1.7 - - - +
70H VAL* 3.8 24.5 - - + +
71H ALA* 5.1 5.5 + - - +
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Residues in contact with LEU 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H TYR* 3.1 38.5 + - + +
13H LEU* 3.7 15.5 - - + +
14H ASN 3.3 0.2 - - - -
15H GLN* 1.3 76.7 - - - +
17H ARG* 1.3 61.0 + - - +
20H LYS* 3.3 3.8 + - - -
21H ILE* 3.1 54.1 + - + +
23H ALA* 4.6 7.0 - - + -
36H ARG* 5.5 0.2 - - - +
37H VAL* 4.0 18.2 + - + +
64H PHE* 3.9 27.1 - - + -
66H PRO* 3.9 22.2 - - + -
70H VAL* 3.9 13.5 - - + -
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Residues in contact with ARG 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H LEU 3.3 11.9 + - - +
14H ASN* 2.6 41.9 + - - +
16H LEU* 1.3 78.9 - - - +
18H LYS* 1.3 93.9 + - - +
20H LYS* 3.5 15.5 + - - +
37H VAL* 3.3 31.9 - - + +
38H VAL 3.2 23.6 + - - +
39H SER* 4.5 6.1 - - - +
40H PHE* 4.9 6.1 - - - -
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Residues in contact with LYS 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H TYR* 6.2 0.2 - - - -
14H ASN* 2.7 42.7 + - - +
15H GLN* 3.0 30.1 + - - +
17H ARG* 1.3 97.1 - - - +
19H GLU* 1.3 63.9 + - + +
20H LYS* 3.1 14.0 + - - +
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Residues in contact with GLU 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H GLN* 2.9 42.2 + - + +
18H LYS* 1.3 74.0 - - + +
20H LYS* 1.3 69.7 + - - +
21H ILE* 3.1 25.6 + - + +
68H LYS* 5.4 4.8 + - - +
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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