Contacts of the helix formed by residues 17 - 25 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A GLY 5.0 6.1 - - - -
12B ASP 3.6 14.8 - - - +
13B TRP 5.7 0.2 - - - -
15B GLY 3.5 0.6 - - - -
16B ARG* 1.3 123.8 - - + +
18B ASN* 1.3 62.9 + - - +
19B HIS 3.2 3.1 - - - -
20B VAL* 3.0 20.9 + - + +
21B LYS* 3.0 30.0 + - + +
42B LEU* 3.5 28.3 - - + -
46B LEU* 4.0 24.0 - - + +
68B ALA 3.4 18.8 - - - -
69B LEU* 3.6 16.4 - - + -
71B GLY* 3.3 34.1 - - - -
72B PHE 5.4 0.4 - - - -
73B ARG* 4.1 9.9 - - + +
115B VAL* 5.4 2.0 - - + -
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Residues in contact with ASN 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLU* 3.8 22.9 + - - +
15B GLY* 2.7 40.0 - - - +
16B ARG 3.2 3.4 + - - -
17B TRP* 1.3 77.5 + - - +
19B HIS* 1.3 61.9 + - - +
20B VAL 2.9 6.4 + - - -
21B LYS* 3.5 20.5 + - - +
22B LYS* 3.6 38.6 + - - +
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Residues in contact with HIS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLU* 3.4 56.3 + - + +
69A ASP* 5.5 2.6 + - - -
71A GLY 6.2 0.2 - - - -
72A ASN* 3.1 33.7 + - + +
487A ALA 5.4 0.6 + - - -
488A ALA* 4.1 11.7 - - + -
489A GLU* 3.0 45.7 + - - +
490A PRO* 4.2 11.5 - - + +
491A HIS 5.4 0.4 - - - +
16B ARG 4.5 2.9 + - - +
17B TRP 3.2 1.6 - - - -
18B ASN* 1.3 76.7 + - + +
20B VAL* 1.3 65.8 + - + +
22B LYS* 5.5 2.9 - - - -
23B PHE* 3.7 18.7 - - - -
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B TRP* 3.5 29.8 - - + +
18B ASN 2.9 1.2 + - - -
19B HIS* 1.3 88.8 - - + +
21B LYS* 1.3 68.6 + - - +
22B LYS 3.2 1.8 - - - -
23B PHE* 3.0 18.8 + - - +
24B LEU* 3.3 24.1 + - + +
42B LEU* 4.5 7.9 - - + -
69B LEU 4.2 9.4 - - - +
70B SER* 3.4 28.0 - - - +
308B PHE* 3.6 22.0 - - + -
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Residues in contact with LYS 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B TRP* 3.0 27.1 + - - +
18B ASN* 3.5 14.3 + - - +
20B VAL* 1.3 76.4 - - - +
22B LYS* 1.3 55.7 + - + +
24B LEU* 2.7 13.4 + - - +
25B GLU* 2.6 73.4 + - + +
39B THR 6.1 0.9 - - - -
42B LEU* 4.0 28.0 - - + +
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Residues in contact with LYS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLU* 4.4 10.3 + - - -
445A VAL* 3.5 30.7 + - - +
447A ASN* 4.6 4.7 - - - +
484A ARG* 3.9 18.9 + - - +
485A TYR* 3.7 20.0 - - - +
486A GLY* 3.6 17.4 + - - +
487A ALA 5.4 0.2 + - - -
488A ALA* 3.9 11.2 - - + +
18B ASN* 3.6 37.5 + - - +
19B HIS* 5.4 2.4 + - - -
20B VAL 3.2 0.6 - - - -
21B LYS* 1.3 77.0 - - + +
23B PHE* 1.3 67.8 + - + +
25B GLU* 5.1 0.4 - - - -
26B ARG* 3.4 48.0 - - - +
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Residues in contact with PHE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLY* 4.2 11.4 - - - -
158A LEU* 3.9 23.3 - - + -
484A ARG* 2.8 29.7 + - + +
485A TYR* 4.1 13.7 - + - -
488A ALA* 4.1 14.8 - - + -
490A PRO* 3.4 33.2 - - + -
19B HIS 3.7 15.9 - - - -
20B VAL* 3.0 16.0 + - - +
21B LYS 2.8 1.6 + - - -
22B LYS* 1.3 80.7 - - + +
24B LEU* 1.3 62.0 + - - +
26B ARG 4.3 1.6 - - - -
35B PHE* 3.5 9.9 - - - -
308B PHE* 4.5 16.4 - + + -
314B ALA* 3.6 14.3 - - + +
315B TYR* 3.5 30.1 - + - -
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B VAL* 3.4 30.7 - - + +
21B LYS* 2.7 7.1 + - - +
23B PHE* 1.3 85.4 - - - +
25B GLU* 1.3 61.1 + - + +
26B ARG 3.4 0.4 - - - -
35B PHE* 3.5 17.8 - - + -
38B SER 3.2 23.7 + - - +
41B SER* 4.0 18.9 + - - -
42B LEU* 3.9 35.0 - - + +
45B LEU* 4.5 4.3 - - + -
308B PHE* 3.7 11.0 - - + -
312B THR* 3.4 42.0 - - + +
314B ALA* 4.4 2.2 - - + -
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Residues in contact with GLU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A ASN* 2.7 33.7 + - - +
21B LYS* 2.6 62.6 + - + +
24B LEU* 1.3 75.1 - - + +
26B ARG* 1.3 61.4 + - + +
27B SER 4.1 0.2 + - - -
37B PRO* 3.7 15.3 - - - +
38B SER 3.7 17.4 - - - +
39B THR* 3.6 27.0 + - - +
42B LEU* 6.4 1.1 - - + -
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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