Contacts of the helix formed by residues 13 - 23 (chain B) in PDB entry 4H0N
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 13 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLU* 4.0 1.6 - - - -
10B SER 2.9 9.7 + - - -
12B ILE* 1.3 80.3 - - - +
14B GLY* 1.3 66.6 + - - +
15B MET 3.5 2.0 - - - -
16B HIS* 3.2 5.5 + - - +
17B CYS* 3.1 29.1 + - - -
42B TYR* 3.5 26.0 - - - -
46B PHE* 4.0 4.2 - - - -
295B PHE* 4.6 1.6 - - - -
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Residues in contact with GLY 14 (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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10B SER 4.1 3.8 + - - -
12B ILE* 3.8 2.2 - - - +
13B GLY* 1.3 75.2 - - - +
15B MET* 1.3 63.5 + - - +
17B CYS* 3.1 6.6 + - - +
18B ALA* 3.0 21.0 + - - +
295B PHE* 4.1 19.1 - - - -
317B SER* 4.5 2.8 + - - -
318B VAL* 3.6 26.0 - - - -
320B VAL* 3.8 4.2 - - - +
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Residues in contact with MET 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLU* 3.3 23.9 + - + +
8B LEU 5.7 1.3 - - - +
10B SER* 6.2 0.7 - - - -
13B GLY 3.5 0.2 - - - -
14B GLY* 1.3 73.8 - - - +
16B HIS* 1.3 56.5 + - - +
18B ALA* 3.2 7.6 + - - +
19B TRP* 2.8 29.6 + - - +
73B LEU* 4.1 26.0 - - + +
74B MET 3.4 35.9 - - - +
75B SER* 4.2 8.7 - - - +
115B LEU* 4.0 20.2 - - + -
117B GLU* 4.1 11.4 - - + -
318B VAL* 4.2 7.3 - - + +
323B ILE* 3.6 36.1 - - + -
327B LEU* 4.8 0.3 - - - +
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Residues in contact with HIS 16 (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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7B GLU* 3.3 16.5 + - - +
13B GLY 3.2 9.8 + - - +
14B GLY 3.1 0.6 - - - -
15B MET* 1.3 79.5 - - - +
17B CYS* 1.3 62.2 + - - +
19B TRP* 3.2 16.4 + + + +
20B LYS* 3.3 25.9 + - + +
28B ILE* 3.5 26.9 - - + +
42B TYR* 2.5 27.5 + - - +
46B PHE* 3.4 36.1 - + + -
49B THR* 3.1 28.7 - - - -
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Residues in contact with CYS 17 (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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13B GLY 3.1 16.9 + - - -
14B GLY 3.1 6.9 + - - +
16B HIS* 1.3 71.7 - - - +
18B ALA* 1.3 65.1 + - - +
20B LYS* 3.1 10.4 + - - +
21B GLU* 3.1 22.7 + - - +
46B PHE* 3.6 21.3 - - - -
295B PHE* 3.9 11.9 - - - -
296B PRO* 4.1 18.6 - - + +
299B TYR* 3.8 22.0 - - - -
320B VAL* 3.7 19.6 - - + +
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Residues in contact with ALA 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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14B GLY 3.0 12.5 + - - +
15B MET 3.4 9.0 - - - +
17B CYS* 1.3 76.8 - - - +
19B TRP* 1.3 60.4 - - - +
21B GLU* 3.4 1.0 + - - -
22B SER* 3.1 24.4 + - - -
320B VAL* 3.5 30.7 - - + +
323B ILE* 3.5 28.0 - - + -
324B SER* 3.7 9.3 - - - +
327B LEU* 3.5 4.6 - - + +
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Residues in contact with TRP 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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3B HIS* 4.2 11.7 - - + -
5B ILE* 3.3 32.5 - - + -
15B MET 2.8 14.8 + - - +
16B HIS* 3.5 14.4 - + - +
17B CYS 3.2 0.4 - - - -
18B ALA* 1.3 76.6 - - - +
20B LYS* 1.3 68.1 + - + +
22B SER* 2.7 18.7 + - - -
23B GLY* 3.8 2.9 + - - -
24B LEU* 3.4 50.9 + - + +
25B ASP 3.5 9.9 - - - -
26B GLY* 2.7 47.1 + - - -
27B GLU* 4.9 2.0 - - - -
28B ILE* 4.5 13.2 - - + -
71B THR* 5.2 0.4 - - + -
73B LEU* 4.7 5.4 - - + -
327B LEU* 3.8 19.0 - - + +
331B PHE* 3.8 20.6 - + - -
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Residues in contact with LYS 20 (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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225A THR* 3.3 21.9 - - - +
16B HIS* 3.3 31.1 + - + +
17B CYS* 3.1 10.8 + - - +
19B TRP* 1.3 83.4 - - + +
21B GLU* 1.3 61.3 + - - +
22B SER 3.4 0.5 + - - -
23B GLY* 3.4 6.8 + - - -
46B PHE* 4.6 15.3 - - + -
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Residues in contact with GLU 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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193A SER* 5.7 0.7 - - - -
225A THR* 4.1 22.8 + - - +
227A LYS* 3.3 38.4 - - - +
252A ARG* 5.0 1.2 + - - -
17B CYS 3.1 15.5 + - - +
18B ALA* 3.9 3.8 - - - +
19B TRP 3.4 0.2 - - - -
20B LYS* 1.3 76.3 - - - +
22B SER* 1.3 61.1 + - - +
23B GLY 3.3 0.7 + - - -
320B VAL* 4.7 9.6 - - + -
321B LYS* 5.7 8.9 + - + +
324B SER* 3.3 23.5 + - - +
328B LYS* 4.5 8.5 + - - +
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Residues in contact with SER 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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252A ARG* 3.7 11.8 + - - -
18B ALA 3.1 13.1 + - - -
19B TRP* 2.7 23.7 + - - -
21B GLU* 1.3 79.5 - - - +
23B GLY* 1.3 58.7 + - - +
24B LEU* 3.3 36.0 + - - +
324B SER* 3.8 20.8 + - - -
327B LEU* 4.1 4.3 - - - -
328B LYS* 3.6 23.7 - - - +
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Residues in contact with GLY 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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223A TYR* 6.5 0.7 - - - -
225A THR* 4.2 16.4 - - - -
251A PRO* 4.1 5.1 - - - +
252A ARG* 3.5 32.9 + - - +
253A GLU 4.3 1.2 + - - -
19B TRP 3.8 0.6 + - - -
20B LYS 3.4 10.9 + - - -
21B GLU 3.3 4.0 - - - -
22B SER* 1.3 79.1 + - - +
24B LEU* 1.3 65.2 + - - +
25B ASP 4.0 0.2 + - - -
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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