Contacts of the helix formed by residues 11 - 22 (chain D) in PDB entry 4NE1
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 ARG 11 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C ALA* 3.3 20.8 + - - +
25C TYR* 3.0 40.3 - - - +
26C THR* 2.5 32.1 + - - +
9D GLY 3.5 4.6 + - - +
10D PHE* 1.3 71.8 - - - +
12D LYS* 1.3 60.3 + - - +
13D GLU* 3.3 4.5 - - + +
14D LEU* 3.2 25.2 + - + +
15D VAL* 3.1 28.6 + - - +
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Residues in contact with LYS 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D PHE 4.2 3.4 - - - +
11D ARG* 1.3 70.0 - - - +
13D GLU* 1.3 63.9 - - - +
15D VAL* 3.6 0.8 + - - +
16D SER* 3.3 18.4 + - - -
32D GLY* 4.0 13.1 + - - -
35D LEU* 3.5 22.2 - - + +
36D GLN* 3.1 46.0 - - + +
39D VAL* 3.5 26.7 - - + -
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Residues in contact with GLU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ARG* 5.0 8.7 + - - -
11D ARG* 4.4 4.2 - - + +
12D LYS* 1.3 77.8 - - - +
14D LEU* 1.3 66.9 + - - +
16D SER* 3.4 5.8 + - - -
17D ARG* 3.2 61.6 + - + +
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Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ARG* 4.9 2.5 - - - +
19C LEU* 4.4 13.6 - - + +
22C ALA* 3.9 30.3 - - + +
23C VAL* 4.0 19.1 - - + -
26C THR* 4.4 14.1 - - - +
10D PHE* 3.9 29.6 - - + -
11D ARG* 3.2 26.6 + - + +
13D GLU* 1.3 85.2 + - - +
15D VAL* 1.3 60.7 + - - +
17D ARG* 3.6 2.6 + - - +
18D LEU* 3.1 47.5 + - + +
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Residues in contact with VAL 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C CYS* 6.0 0.4 - - - -
10D PHE* 4.1 14.6 - - + -
11D ARG 3.1 15.6 + - - +
12D LYS 3.6 2.7 + - - +
13D GLU 3.4 0.2 - - - -
14D LEU* 1.3 76.9 - - + +
16D SER* 1.3 56.7 + - - +
18D LEU* 3.6 7.2 - - - +
19D LEU* 2.9 43.3 + - + +
35D LEU* 3.6 21.5 - - + -
38D MET* 4.0 19.5 - - + -
39D VAL* 3.9 20.6 - - + +
42D LEU* 3.8 29.6 - - + -
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Residues in contact with SER 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LYS 3.3 17.0 + - - -
13D GLU* 3.8 5.8 - - - -
14D LEU 3.4 0.2 - - - -
15D VAL* 1.3 73.5 - - - +
17D ARG* 1.3 63.1 + - - +
19D LEU* 3.4 3.8 + - - +
20D HIS* 2.9 44.7 + - - +
30D VAL* 5.5 3.9 - - - +
35D LEU* 3.7 22.5 - - - +
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Residues in contact with ARG 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C TYR* 4.0 27.4 + - + -
18C ARG* 5.9 1.1 - - - +
19C LEU* 4.9 13.2 - - + -
13D GLU* 3.2 48.3 + - + +
14D LEU* 4.3 2.2 - - - +
16D SER* 1.3 77.5 - - - +
18D LEU* 1.3 64.2 + - - +
20D HIS* 3.4 5.7 + - - +
21D LEU* 3.1 34.2 + - + +
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Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 4.0 24.2 - - + +
23C VAL* 3.6 23.6 - - + -
55C PHE* 3.9 30.5 - - + -
58C CYS* 3.6 42.8 - - + +
59C GLU* 6.0 0.2 - - - -
62C ALA* 4.9 0.5 - - - +
14D LEU* 3.1 39.0 + - + +
15D VAL* 3.6 8.3 - - - +
17D ARG* 1.3 78.3 - - - +
19D LEU* 1.3 62.9 + - + +
21D LEU* 3.7 17.1 + - + +
22D HIS* 4.4 3.6 + - - +
42D LEU* 4.9 4.0 - - + -
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C CYS* 4.1 11.9 - - + +
61C PHE* 4.6 6.3 - - + -
62C ALA* 3.4 45.1 - - + +
65C LEU* 3.8 22.4 - - + -
15D VAL* 2.9 31.3 + - + +
16D SER 3.8 3.8 - - - +
17D ARG 3.4 0.2 - - - -
18D LEU* 1.3 78.1 - - + +
20D HIS* 1.3 59.7 + - - +
21D LEU 3.4 0.9 + - - -
22D HIS 3.7 0.9 + - - -
23D PHE* 3.4 30.1 + - + -
30D VAL* 3.6 27.8 - - + -
35D LEU* 3.7 18.8 - - + -
38D MET* 4.6 6.1 - - + -
42D LEU* 6.5 0.2 - - + -
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Residues in contact with HIS 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D SER* 2.9 37.6 + - - +
17D ARG* 3.4 6.9 + - - +
19D LEU* 1.3 71.5 - - - +
21D LEU* 1.3 62.6 + - - +
22D HIS 3.6 0.2 + - - -
23D PHE* 3.6 29.7 + + - +
26D ASP* 4.9 13.5 + - - +
28D THR 2.9 28.6 + - - -
29D LYS* 3.9 19.7 - - + +
30D VAL* 4.7 5.5 + - + -
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Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C TYR* 5.2 9.4 - - + -
16C GLN* 3.8 22.0 - - + +
19C LEU* 3.0 37.5 - - + -
55C PHE* 5.2 1.8 - - + -
17D ARG* 3.1 24.9 + - + +
18D LEU* 4.0 15.5 - - + +
19D LEU 3.4 1.2 - - - -
20D HIS* 1.3 76.9 - - - +
22D HIS* 1.3 78.3 + - + +
23D PHE 5.3 0.3 - - - +
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Residues in contact with HIS 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLN* 3.4 29.8 + - - -
55C PHE* 6.2 0.4 - + - -
59C GLU* 4.7 24.7 + - + +
62C ALA* 4.9 3.4 - - + -
63C LYS* 2.8 52.5 + - - +
18D LEU 4.4 3.6 + - - +
19D LEU 3.7 6.3 + - - -
20D HIS 3.5 0.2 - - - -
21D LEU* 1.3 85.4 + - + +
23D PHE* 1.3 61.2 + - - +
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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