Contacts of the helix formed by residues 7 - 19 (chain I) 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 GLY 7 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41E ASP* 3.5 8.6 - - - +
5I GLY* 3.2 8.1 - - - -
6I GLN* 1.3 78.0 - - - +
8I LEU* 1.3 65.6 + - - +
10I ASP* 4.3 1.2 - - - +
11I TYR* 3.4 21.1 + - - +
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Residues in contact with LEU 8 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E SER* 3.2 31.9 - - - +
40E PHE* 3.3 39.3 - - - +
41E ASP* 3.4 6.1 - - + +
44E THR* 3.6 20.9 - - - +
46E LEU* 4.0 22.0 - - + +
55E LEU* 4.5 5.4 - - + -
7I GLY* 1.3 73.5 - - - +
9I GLN* 1.3 57.3 + - - +
10I ASP 3.3 0.2 - - - -
11I TYR* 3.6 7.4 - - + +
12I TYR* 2.5 45.0 + - + +
72I LEU* 5.5 10.8 - - + -
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Residues in contact with GLN 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E ASP* 3.4 15.7 + - - +
43E PHE* 3.4 25.5 - - - +
44E THR* 3.5 22.0 - - + +
55E LEU* 5.0 4.3 - - + -
57E PHE* 3.8 9.5 - - + -
6I GLN* 4.6 4.2 - - - +
7I GLY 3.4 0.8 - - - -
8I LEU* 1.3 81.0 - - - +
10I ASP* 1.3 69.0 + - - +
12I TYR* 4.5 3.8 - - - -
13I LEU* 3.2 37.0 + - + +
58I LYS* 2.3 41.4 + - - +
28Z U 2.8 20.5 + - - +
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Residues in contact with ASP 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I GLN* 3.6 46.6 + - - +
7I GLY 3.9 2.1 + - - +
9I GLN* 1.3 86.6 - - - +
11I TYR* 1.3 62.0 + - - +
14I ASN* 3.2 23.0 + - - +
40I PHE* 3.4 21.4 - - + -
42I ASN* 5.3 0.9 - - - +
58I LYS* 5.0 1.9 + - - -
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Residues in contact with TYR 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I GLY 3.4 18.1 + - - +
8I LEU* 3.2 8.4 + - + +
10I ASP* 1.3 78.2 - - - +
12I TYR* 1.3 64.9 + + + +
14I ASN* 3.1 10.2 + - + +
15I GLN* 2.9 59.0 + - + +
70I VAL* 4.4 3.8 - - + -
71I ALA* 2.7 32.7 + - - +
72I LEU* 4.0 31.2 + - + -
73I ASN* 4.9 15.2 + - + -
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Residues in contact with TYR 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E LEU* 3.5 32.5 - - + +
53E GLN* 2.6 38.7 + - - +
55E LEU* 3.6 36.1 - - + -
8I LEU* 2.5 24.6 + - + +
9I GLN 4.2 0.4 - - - +
11I TYR* 1.3 79.5 - + + +
13I LEU* 1.3 59.1 + - - +
15I GLN* 3.2 5.6 + - - +
16I LEU* 2.9 61.8 + - + +
64I PHE* 4.9 1.5 + - + -
66I PRO* 3.2 25.0 - - + +
70I VAL* 4.0 16.1 - - + +
72I LEU* 5.5 5.8 - - + -
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Residues in contact with LEU 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E LEU* 4.4 8.5 - - + -
57E PHE* 5.0 2.9 - - + -
9I GLN* 3.2 39.9 + - + +
12I TYR* 1.3 79.4 - - - +
14I ASN* 1.3 61.3 + - - +
16I LEU* 3.7 18.2 + - + +
17I ARG* 3.2 21.7 + - - +
37I VAL* 3.7 16.0 - - + +
40I PHE* 3.6 36.8 - - + -
45I VAL* 4.5 10.1 - - + -
58I LYS* 4.4 9.0 - - - -
64I PHE* 3.9 33.7 - - + -
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Residues in contact with ASN 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I ASP 3.2 19.9 + - - +
11I TYR* 3.1 10.8 + - + +
12I TYR 3.1 0.4 - - - -
13I LEU* 1.3 77.6 - - - +
15I GLN* 1.3 54.7 + - - +
17I ARG* 2.3 37.3 + - - +
18I LYS* 2.5 57.2 + - - +
40I PHE* 3.7 11.4 - - + -
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Residues in contact with GLN 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I TYR* 2.9 48.2 + - + +
12I TYR 3.6 3.8 - - - +
14I ASN* 1.3 73.7 + - + +
16I LEU* 1.3 59.0 + - - +
17I ARG 3.0 1.8 - - - -
18I LYS* 3.9 28.5 + - - +
19I GLU* 2.4 77.9 + - + +
70I VAL* 3.5 30.4 - - + +
71I ALA* 4.8 3.0 + - - +
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Residues in contact with LEU 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I TYR* 2.9 44.2 + - + +
13I LEU* 3.8 23.6 - - + +
15I GLN* 1.3 75.3 - - - +
17I ARG* 1.3 59.6 + - - +
20I LYS* 3.3 3.8 + - - -
21I ILE* 3.2 47.9 + - + +
23I ALA* 4.9 7.0 - - + -
36I ARG* 5.5 0.3 - - - +
37I VAL* 3.9 20.3 + - + +
64I PHE* 4.2 18.2 - - + -
66I PRO* 3.9 13.5 - - + -
70I VAL* 3.7 24.0 - - + -
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Residues in contact with ARG 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I LEU 3.2 12.4 + - - +
14I ASN* 2.3 45.7 + - - +
15I GLN 3.0 0.2 - - - -
16I LEU* 1.3 79.1 - - - +
18I LYS* 1.3 87.4 + - - +
20I LYS* 3.5 15.2 + - - +
37I VAL* 3.5 22.0 - - + +
38I VAL* 3.3 28.9 + - - +
39I SER* 4.6 7.2 - - - +
40I PHE* 4.8 7.0 - - - -
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Residues in contact with LYS 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I ASN* 2.5 41.6 + - - +
15I GLN* 3.7 25.1 + - - +
17I ARG* 1.3 94.5 - - - +
19I GLU* 1.3 62.0 + - + +
20I LYS* 3.1 14.8 + - - +
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Residues in contact with GLU 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I GLN* 2.4 64.9 + - - +
18I LYS* 1.3 67.3 - - + +
20I LYS* 1.3 69.0 + - - +
21I ILE* 2.9 28.2 + - + +
68I LYS* 3.6 25.1 + - - -
69I ASN 4.8 0.5 - - - +
70I VAL* 4.4 3.5 - - - +
71I ALA* 4.1 20.6 + - - +
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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