Contacts of the helix formed by residues 17 - 25 (chain H) in PDB entry 1R4N
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 TRP 17 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71G GLY 4.9 7.0 - - - -
12H ASP 3.7 14.6 - - - +
13H TRP 5.7 0.4 - - - -
15H GLY 3.5 0.2 - - - -
16H ARG* 1.3 124.9 - - + +
18H ASN* 1.3 64.1 + - - +
19H HIS 3.2 2.9 - - - -
20H VAL* 3.0 20.5 + - + -
21H LYS* 3.0 29.9 + - + +
42H LEU* 3.5 30.7 - - + -
46H LEU* 4.0 22.7 - - + +
68H ALA 3.4 18.6 - - - -
69H LEU* 3.6 17.9 - - + -
71H GLY* 3.3 34.3 - - - -
72H PHE 5.4 0.4 - - - -
73H ARG* 4.1 10.9 - - + +
115H VAL* 5.4 1.8 - - + -
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Residues in contact with ASN 18 (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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68G GLU* 3.7 25.5 + - + +
15H GLY* 2.7 41.5 - - - +
16H ARG 3.2 3.2 + - - -
17H TRP* 1.3 72.2 + - - +
19H HIS* 1.3 60.0 + - - +
20H VAL 2.9 11.7 + - - -
21H LYS* 3.5 20.5 + - - +
22H LYS* 3.6 39.1 + - - +
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Residues in contact with HIS 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G GLU* 3.3 56.5 + - + +
69G ASP* 5.4 2.8 + - - -
72G ASN* 3.0 35.6 + - + +
487G ALA 5.4 0.8 + - - -
488G ALA* 4.2 10.4 - - + -
489G GLU* 3.1 45.5 + - - +
490G PRO* 4.2 11.4 - - + +
491G HIS 5.4 0.4 - - - +
16H ARG 4.9 2.5 + - - +
17H TRP* 3.2 1.8 - - - +
18H ASN* 1.3 75.3 + - + +
20H VAL* 1.3 66.3 + - + +
22H LYS* 5.4 3.6 + - - -
23H PHE* 3.8 19.1 - - - -
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Residues in contact with VAL 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H TRP* 3.5 28.5 - - + +
18H ASN 2.9 1.0 + - - -
19H HIS* 1.3 91.2 - - + +
21H LYS* 1.3 68.1 + - - +
22H LYS 3.1 1.8 - - - -
23H PHE* 2.9 18.7 + - - +
24H LEU* 3.3 22.3 + - + +
42H LEU* 4.5 7.9 - - + -
69H LEU 4.1 9.6 - - - +
70H SER* 3.3 30.1 - - - +
308H PHE* 3.6 22.4 - - + -
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Residues in contact with LYS 21 (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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17H TRP* 3.0 27.6 + - - +
18H ASN* 3.5 14.3 + - - +
20H VAL* 1.3 77.0 - - - +
22H LYS* 1.3 54.1 + - + +
24H LEU* 2.7 12.8 + - - +
25H GLU* 2.6 72.5 + - + +
39H THR 6.1 1.1 - - - -
42H LEU* 4.0 27.8 - - + -
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Residues in contact with LYS 22 (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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68G GLU* 4.3 17.2 + - - -
445G VAL* 3.6 29.9 + - - +
447G ASN* 4.6 4.5 - - - +
484G ARG* 4.0 17.6 + - - +
485G TYR 3.8 18.4 - - - +
486G GLY* 3.7 14.8 + - - +
487G ALA 5.3 0.2 - - - -
488G ALA* 3.8 12.1 - - + +
18H ASN* 3.6 32.6 + - - +
19H HIS* 5.4 2.6 + - - -
20H VAL 3.1 0.8 - - - -
21H LYS* 1.3 77.3 - - + +
23H PHE* 1.3 67.8 + - + +
25H GLU* 5.1 0.2 - - - -
26H ARG* 3.4 49.4 - - - +
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Residues in contact with PHE 23 (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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157G GLY* 4.2 11.0 - - - -
158G LEU* 3.9 24.2 - - + -
484G ARG* 2.9 27.5 + - + +
485G TYR* 4.2 11.9 - + - -
488G ALA* 4.0 15.5 - - + -
490G PRO* 3.3 34.8 - - + -
19H HIS 3.8 15.7 - - - -
20H VAL* 2.9 14.5 + - - +
21H LYS 2.8 1.0 + - - -
22H LYS* 1.3 82.0 - - + +
24H LEU* 1.3 61.5 + - - +
26H ARG 4.3 1.3 - - - -
35H PHE* 3.5 9.0 - - - -
308H PHE* 4.5 15.0 - + + -
314H ALA* 3.6 14.8 - - + +
315H TYR* 3.5 29.4 - + - -
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Residues in contact with LEU 24 (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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20H VAL* 3.4 31.2 - - + +
21H LYS* 2.7 6.5 + - - +
23H PHE* 1.3 86.2 - - - +
25H GLU* 1.3 60.4 + - + +
26H ARG 3.4 0.7 - - - -
35H PHE* 3.5 16.7 - - + -
38H SER 3.2 23.3 + - - +
41H SER* 4.0 19.0 + - - -
42H LEU* 3.9 35.0 - - + +
45H LEU* 4.5 3.1 - - + -
308H PHE* 3.7 11.0 - - + -
312H THR* 3.4 42.0 - - + +
314H ALA* 4.4 2.5 - - + -
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Residues in contact with GLU 25 (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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447G ASN* 2.7 33.8 + - - +
21H LYS* 2.6 62.6 + - + +
24H LEU* 1.3 75.2 - - + +
26H ARG* 1.3 60.3 - - + +
37H PRO* 3.8 15.0 - - - +
38H SER 3.7 17.6 - - - +
39H THR* 3.6 26.6 + - - +
42H LEU* 6.4 1.6 - - + -
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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