Contacts of the helix formed by residues 12 - 30 (chain H) in PDB entry 5PRC
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 ILE 12 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H GLY* 2.9 32.8 + - - +
6H LEU* 3.8 26.9 - - + +
11H ASP* 1.3 68.3 - - - +
13H ALA* 1.3 70.2 + - - +
15H LEU* 2.9 17.5 + - + +
16H VAL* 3.0 28.5 + - + +
284M LEU* 4.1 4.7 - - + -
288M PHE* 4.0 37.0 - - + -
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Residues in contact with ALA 13 (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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11H ASP* 3.5 2.3 + - - +
12H ILE* 1.3 78.0 - - - +
14H GLN* 1.3 57.8 + - - +
16H VAL* 3.1 2.6 + - - -
17H TRP* 2.8 26.3 + - - +
199M TRP* 3.3 9.0 - - + -
284M LEU* 4.1 27.8 - - + +
288M PHE* 5.0 1.8 + - - +
289M VAL* 3.6 31.2 - - + -
292M TRP* 4.2 4.3 - - + -
295M TRP* 3.8 19.3 - - + +
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Residues in contact with GLN 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H HIS 3.7 6.7 + - - +
10H LEU* 3.4 22.0 - - - +
11H ASP* 3.1 38.6 + - - +
12H ILE 2.9 0.6 + - - -
13H ALA* 1.3 79.1 - - - +
15H LEU* 1.3 64.5 + - - +
17H TRP* 3.4 13.0 - - - +
18H TYR* 3.1 34.2 + - + +
702L LDA 5.2 7.1 - - + +
295M TRP* 3.7 12.1 - - + -
299M HIS* 3.5 33.1 + - + +
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Residues in contact with LEU 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H LEU* 3.2 34.8 - - + -
10H LEU* 4.0 27.1 - - + -
11H ASP 3.5 9.4 - - - +
12H ILE* 2.9 10.1 + - + +
14H GLN* 1.3 80.2 - - + +
16H VAL* 1.3 61.5 + - + +
18H TYR* 3.0 30.4 + - + +
19H ALA* 3.1 12.4 + - - +
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Residues in contact with VAL 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H ILE* 3.0 28.0 + - + +
13H ALA* 3.5 9.4 - - - +
15H LEU* 1.3 75.6 - - + +
17H TRP* 1.3 65.6 + - - +
19H ALA* 4.4 9.4 - - + -
20H GLN* 2.9 25.3 + - + +
199M TRP* 3.5 15.3 - - + +
280M VAL* 4.2 18.6 - - + -
284M LEU* 4.4 8.3 - - + -
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Residues in contact with TRP 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H ALA 2.8 11.9 + - - +
14H GLN* 3.4 13.2 - - - +
15H LEU 3.2 0.4 - - - -
16H VAL* 1.3 79.3 - - - +
18H TYR* 1.3 92.8 + + - +
20H GLN* 3.3 2.8 + - - +
21H TRP* 3.2 54.0 + + - +
62L PHE* 4.3 20.9 - + - -
702L LDA 3.8 52.3 - - + +
198M PRO* 3.5 34.6 - - + +
199M TRP* 3.4 9.8 - + + -
202M PHE* 3.9 15.5 - + - -
295M TRP* 4.8 3.4 - - + -
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Residues in contact with TYR 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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14H GLN* 3.1 44.9 + - + -
15H LEU* 3.0 19.6 + - + +
17H TRP* 1.3 104.2 - + - +
19H ALA* 1.3 65.5 + - - +
21H TRP* 3.4 7.5 + + + +
22H LEU* 3.2 33.7 + - + +
702L LDA 4.3 12.7 - - + +
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Residues in contact with ALA 19 (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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15H LEU 3.1 9.1 + - - +
16H VAL* 3.8 13.0 - - + +
18H TYR* 1.3 76.3 - - - +
20H GLN* 1.3 65.4 + - - +
22H LEU* 3.0 9.7 + - - +
23H VAL* 2.9 31.1 + - + +
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Residues in contact with GLN 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H VAL* 2.9 20.5 + - + +
17H TRP 3.4 6.1 - - - +
18H TYR 3.2 0.2 - - - -
19H ALA* 1.3 79.7 - - - +
21H TRP* 1.3 61.3 + - - +
23H VAL* 3.2 7.7 + - - +
24H ILE* 3.2 32.5 + - + +
199M TRP* 2.9 28.5 + - - +
202M PHE* 3.3 31.6 - - + -
273M MET* 3.6 29.3 - - - +
276M VAL* 5.7 1.1 - - - +
277M SER* 3.6 14.6 + - - +
280M VAL* 4.6 10.0 - - - +
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Residues in contact with TRP 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H TRP* 3.2 58.3 + + - +
18H TYR* 3.7 10.3 - + + +
19H ALA 3.3 0.2 - - - -
20H GLN* 1.3 81.1 - - - +
22H LEU* 1.3 62.3 + - + +
24H ILE* 3.7 16.2 - - + +
25H TRP* 3.1 71.3 + + + -
701H LDA 4.6 22.7 - - + -
705L LDA 6.1 3.6 - - + -
202M PHE* 3.5 31.6 - + - -
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Residues in contact with LEU 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H TYR* 3.2 24.9 + - + +
19H ALA* 3.0 12.8 + - - +
21H TRP* 1.3 78.0 - - + +
23H VAL* 1.3 64.7 + - + +
24H ILE 3.1 0.2 - - - -
25H TRP* 4.5 2.6 - - - +
26H THR* 2.6 41.1 + - - +
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Residues in contact with VAL 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ALA* 2.9 21.5 + - + +
20H GLN* 3.5 10.1 - - - +
22H LEU* 1.3 76.5 - - + +
24H ILE* 1.3 62.5 + - + +
26H THR* 3.4 4.8 - - - -
27H VAL* 2.9 42.1 + - + +
269M PHE* 6.0 2.0 - - + -
273M MET* 5.3 10.3 - - + -
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Residues in contact with ILE 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H GLN* 3.2 35.6 + - - +
21H TRP* 3.8 18.8 - - + +
22H LEU 3.1 0.2 - - - -
23H VAL* 1.3 79.5 - - + +
25H TRP* 1.3 64.6 + - + +
27H VAL* 3.2 3.5 + - - +
28H VAL* 2.8 45.6 + - + +
701H LDA 4.6 17.7 - - + -
202M PHE* 3.8 25.6 - - + -
206M PHE* 4.0 17.3 - - + -
269M PHE* 4.9 7.4 - - + -
273M MET* 4.3 16.4 - - + -
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Residues in contact with TRP 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H TRP* 3.1 57.5 + + + +
22H LEU* 4.5 2.2 - - - +
24H ILE* 1.3 80.9 - - + +
26H THR* 1.3 57.8 + - - +
28H VAL* 4.0 22.2 - - + -
29H LEU* 2.8 65.4 + - + +
701H LDA 4.4 33.7 - - + -
705L LDA 4.3 31.2 - - + -
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Residues in contact with THR 26 (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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22H LEU* 2.6 32.3 + - - +
23H VAL* 3.4 5.4 - - - -
25H TRP* 1.3 76.0 - - - +
27H VAL* 1.3 63.8 + - + +
30H LEU* 2.8 57.3 + - + +
31H TYR 3.5 0.5 + - - -
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Residues in contact with VAL 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H VAL* 2.9 34.0 + - + +
24H ILE 3.8 2.2 - - - +
26H THR* 1.3 75.6 - - + +
28H VAL* 1.3 60.7 + - - +
31H TYR* 3.0 25.7 + - + +
32H LEU* 2.9 37.3 + - + +
269M PHE* 3.7 39.7 - - + -
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Residues in contact with VAL 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H ILE* 2.8 30.6 + - + +
25H TRP* 4.0 19.7 - - + +
27H VAL* 1.3 77.6 - - - +
29H LEU* 1.3 58.4 + - + +
32H LEU* 3.4 12.4 + - + +
33H ARG* 2.8 35.9 + - + +
701H LDA 4.0 25.8 - - + -
266M TRP* 3.7 27.6 - - + -
269M PHE* 4.1 22.2 - - + -
270M PHE* 5.6 0.7 - - + -
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Residues in contact with LEU 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H TRP* 2.8 50.6 + - + +
28H VAL* 1.3 75.3 - - + +
30H LEU* 1.3 77.2 + - + +
31H TYR 3.4 0.2 - - - -
33H ARG* 3.6 19.9 - - + +
34H ARG* 4.1 9.0 + - - +
37H ARG* 5.4 0.7 + - - -
701H LDA 4.0 27.4 - - - +
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Residues in contact with LEU 30 (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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26H THR* 2.8 38.1 + - + +
29H LEU* 1.3 91.8 - - + +
31H TYR* 1.3 58.7 + - - +
34H ARG* 3.1 50.1 + - - +
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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
------------------------------------------------------------
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