Contacts of the helix formed by residues 18 - 34 (chain C) in PDB entry 4PEI
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 LYS 18 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C VAL* 3.3 17.4 + - - +
16C HIS* 3.1 14.1 - - + +
17C GLY* 1.3 79.0 - - - +
19C TYR* 1.3 61.9 + - - +
20C ARG 3.4 2.7 - - - -
21C GLU* 3.3 30.9 + - + +
22C MET* 3.1 21.8 + - - +
69C ASP* 3.8 4.0 - - - -
249C LYS* 6.3 1.3 - - - -
250C ILE* 3.8 24.7 + - + +
251C GLY* 4.2 13.3 - - - -
252C TYR* 6.2 1.4 - - - -
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Residues in contact with TYR 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C VAL* 3.8 17.0 - - + -
17C GLY* 3.4 14.1 - - - -
18C LYS* 1.3 74.4 - - - +
20C ARG* 1.3 66.3 + - - +
22C MET* 3.1 23.1 + - + +
23C TYR* 3.0 30.7 + + + -
46C MET* 2.6 59.3 + - + +
48C THR* 3.6 9.0 - - - +
69C ASP* 3.3 5.1 + - + -
70C PHE* 3.9 35.4 - + + -
73C TYR* 3.5 23.6 - + + -
84C THR* 5.7 0.7 - - + -
86C PHE* 5.6 0.2 - - - -
110C MET* 3.7 31.7 - - + -
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Residues in contact with ARG 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR* 1.3 72.1 - - - +
21C GLU* 1.3 58.1 + - - +
23C TYR* 3.3 2.6 + - - +
24C ARG* 2.8 50.1 + - - +
69C ASP* 2.7 46.1 + - - +
72C LEU* 3.9 16.2 - - - +
73C TYR* 3.5 22.7 - - + +
78C GLU* 3.6 30.3 + - - +
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Residues in contact with GLU 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LYS* 3.3 43.7 + - + +
19C TYR 3.2 0.6 - - - -
20C ARG* 1.3 80.7 - - - +
22C MET* 1.3 56.0 + - - +
24C ARG* 3.4 24.2 + - - +
25C GLN* 2.9 49.0 + - + +
69C ASP* 4.3 0.4 + - - -
250C ILE* 4.3 3.4 - - + -
251C GLY* 3.6 25.4 - - - +
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Residues in contact with MET 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C VAL* 4.0 14.8 - - + -
15C VAL* 3.7 26.7 - - + -
18C LYS 3.1 14.4 + - - +
19C TYR* 3.1 34.3 + - + +
21C GLU* 1.3 76.2 - - - +
23C TYR* 1.3 83.2 + - + +
25C GLN* 3.2 6.5 + - - +
26C LEU* 2.9 42.1 + - + +
40C VAL* 4.8 0.7 - - - -
42C CYS* 3.8 17.7 - - - -
84C THR* 5.0 0.9 - - + -
250C ILE* 3.7 26.4 - - + +
256C ILE* 4.3 0.8 - - + +
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Residues in contact with TYR 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR* 3.0 23.8 + - + +
20C ARG 3.9 2.2 - - - +
22C MET* 1.3 94.8 - - + +
24C ARG* 1.3 61.0 + - - +
26C LEU* 3.8 21.2 - - + +
27C SER* 2.4 36.5 + - - -
40C VAL* 5.0 1.1 - - + -
73C TYR* 3.4 34.1 - + - +
80C ALA* 3.5 19.3 - - + +
81C PRO* 3.6 33.7 - - + -
82C TYR* 4.0 8.7 - + - -
84C THR* 2.8 35.7 + - - +
110C MET* 3.8 14.9 - - + +
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Residues in contact with ARG 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ARG* 2.8 40.9 + - - +
21C GLU* 3.4 32.1 - - + +
23C TYR* 1.3 76.8 - - - +
25C GLN* 1.3 63.4 + - + +
27C SER* 3.3 5.7 + - - -
28C GLU* 3.0 33.8 + - + +
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Residues in contact with GLN 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLU* 2.9 45.0 + - + +
22C MET 3.6 4.9 - - - +
24C ARG* 1.3 74.9 - - + +
26C LEU* 1.3 64.9 + - - +
28C GLU* 3.1 9.9 + - - +
29C TYR* 3.0 22.2 + - - +
250C ILE* 4.9 5.6 - - - +
251C GLY* 4.4 15.4 - - - +
252C TYR 5.2 7.3 + - - +
255C ALA* 5.4 0.7 - - - +
256C ILE* 3.3 28.8 - - + +
258C TYR* 4.3 1.9 + - - +
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Residues in contact with LEU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ALA* 3.5 28.5 - - + -
12C VAL* 4.9 1.6 - - + -
22C MET* 2.9 37.5 + - + +
23C TYR* 3.8 18.8 - - + +
25C GLN* 1.3 76.3 - - - +
27C SER* 1.3 62.1 + - - +
29C TYR* 3.0 11.1 + - - +
30C GLU 3.2 9.5 + - - -
37C ILE* 3.4 15.1 - - + +
40C VAL* 3.8 29.8 - - + -
82C TYR* 3.7 16.1 + - + -
256C ILE* 3.8 16.8 - - + -
258C TYR* 3.7 17.3 - - + +
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Residues in contact with SER 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TYR* 2.4 31.2 + - - +
24C ARG* 3.6 5.4 + - - -
26C LEU* 1.3 73.0 - - - +
28C GLU* 1.3 67.1 + - - +
30C GLU* 3.3 5.0 + - - +
31C LYS* 2.9 35.8 + - - +
81C PRO* 5.0 4.0 - - - +
82C TYR* 3.2 18.5 + - - -
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Residues in contact with GLU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ARG* 3.0 24.1 + - + +
25C GLN* 3.3 11.9 - - - +
27C SER* 1.3 78.9 - - - +
29C TYR* 1.3 58.8 + - - +
31C LYS* 4.4 16.0 - - - +
32C SER* 2.9 38.9 + - - -
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Residues in contact with TYR 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C HIS* 3.9 15.6 + - + +
25C GLN 3.0 8.6 + - - +
26C LEU 3.0 4.4 + - - +
28C GLU* 1.3 77.6 - - - +
30C GLU* 1.3 56.1 + - - +
32C SER* 3.0 7.4 + - - -
33C THR* 2.7 61.7 + - + +
35C LYS* 3.1 50.1 + - + +
37C ILE* 3.8 24.5 - - + -
258C TYR* 3.1 70.7 - + + +
260C ASP* 4.4 0.3 + - - -
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Residues in contact with GLU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU 3.2 6.4 + - - +
27C SER* 3.6 7.7 - - - +
29C TYR* 1.3 77.3 - - - +
31C LYS* 1.3 57.4 + - + +
33C THR* 4.2 0.4 - - - -
34C GLY* 2.6 36.0 + - - -
35C LYS 3.2 21.1 - - - +
36C GLU* 3.6 11.3 - - - +
37C ILE* 2.9 40.8 + - + +
82C TYR* 2.7 39.1 + - - -
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Residues in contact with LYS 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C SER* 2.9 27.5 + - - +
28C GLU* 3.7 18.6 - - - +
30C GLU* 1.3 78.3 - - + +
32C SER* 1.3 61.5 + - - +
34C GLY* 4.0 4.5 + - - -
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Residues in contact with SER 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C GLU* 2.9 26.4 + - - -
29C TYR* 3.0 9.5 + - - -
31C LYS* 1.3 80.1 - - - +
33C THR* 1.3 69.3 + - - +
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Residues in contact with THR 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C TYR* 2.7 43.6 + - + +
32C SER* 1.3 84.8 - - - +
34C GLY* 1.3 57.7 + - - +
35C LYS* 2.9 44.9 + - + +
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Residues in contact with GLY 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLU 2.6 21.1 + - - -
31C LYS 4.0 4.3 + - - -
32C SER 3.5 1.8 - - - -
33C THR* 1.3 71.9 - - - +
35C LYS* 1.3 62.1 + - - +
36C GLU* 3.9 1.2 + - - +
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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