Contacts of the helix formed by residues 13 - 34 (chain C) in PDB entry 5DIR
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 LEU 13 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PRO* 2.8 25.0 + - + +
12C TRP* 1.3 73.9 - - - +
14C TRP* 1.3 67.9 + - + +
15C ILE 3.1 3.4 - - - -
16C THR* 3.0 30.1 + - - +
17C VAL* 3.3 17.6 + - + -
88C LEU* 4.7 18.6 - - + -
89C LYS* 6.2 2.0 - - - +
103C ALA* 5.3 3.4 - - - -
106C LEU* 6.2 1.3 - - + -
202C OLC 3.8 28.3 - - + -
203C OLC 4.4 12.6 - - + -
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Residues in contact with TRP 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TRP* 3.0 27.0 + + + +
13C LEU* 1.3 85.1 - - + +
15C ILE* 1.3 61.8 + - + +
16C THR 3.4 0.2 - - - -
17C VAL* 3.9 26.2 - - + +
18C LEU* 3.1 38.7 + - + +
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Residues in contact with ILE 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TRP* 4.6 22.7 - - + +
13C LEU 3.1 0.8 - - - -
14C TRP* 1.3 77.3 - - + +
16C THR* 1.3 60.8 + - - +
18C LEU* 3.3 9.8 + - + +
19C VAL* 2.9 31.3 + - + +
100C ILE* 4.0 36.1 - - + -
103C ALA* 3.9 18.4 - - + -
104C LEU* 3.9 29.2 - - + +
301F OLC 5.4 4.7 - - + -
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Residues in contact with THR 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 3.0 17.8 + - - +
15C ILE* 1.3 78.7 - - - +
17C VAL* 1.3 62.6 + - - +
19C VAL* 3.4 2.1 + - - +
20C PHE* 3.0 23.3 + - + +
88C LEU* 5.5 0.7 - - - +
103C ALA* 2.8 36.1 + - - +
106C LEU* 3.6 35.2 - - + +
107C GLY* 3.7 12.5 - - - -
110C LEU* 4.4 2.9 - - + -
202C OLC 3.9 19.3 - - + -
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Residues in contact with VAL 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 3.3 23.4 + - + +
14C TRP* 3.9 26.7 - - + +
16C THR* 1.3 75.5 - - - +
18C LEU* 1.3 62.5 + - + +
20C PHE* 3.2 6.2 + - - +
21C VAL* 3.0 45.0 + - + +
202C OLC 3.7 34.8 - - + -
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Residues in contact with LEU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C TRP* 3.1 32.3 + - + +
15C ILE* 3.7 8.5 - - + +
17C VAL* 1.3 77.8 - - + +
19C VAL* 1.3 65.2 + - - +
21C VAL* 3.2 10.5 - - + +
22C LEU* 3.0 45.0 + - + +
301F OLC 4.9 8.7 - - + -
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Residues in contact with VAL 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ILE* 2.9 22.3 + - + +
16C THR* 3.7 4.5 - - - +
18C LEU* 1.3 75.0 - - - +
20C PHE* 1.3 59.1 + - - +
22C LEU* 3.8 1.1 - - - +
23C ASP* 2.9 36.0 + - + +
104C LEU* 3.6 32.8 - - + +
107C GLY* 3.7 22.2 - - - +
108C GLY* 3.8 2.5 - - - +
141C LEU* 5.1 4.0 - - + +
142C ALA* 5.1 2.0 - - - -
145C ALA* 3.6 23.3 - - + -
301F OLC 3.7 27.6 - - + -
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Residues in contact with PHE 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C THR* 3.0 18.1 + - + +
17C VAL 3.5 3.6 - - - +
19C VAL* 1.3 76.6 - - - +
21C VAL* 1.3 72.5 + - + +
23C ASP* 3.2 7.7 + - - +
24C GLN* 3.0 46.8 + - + +
107C GLY* 4.2 9.9 - - - +
110C LEU* 3.5 26.2 - - + -
111C GLY* 3.7 20.4 - - - -
114C TYR* 3.9 26.5 - + + -
202C OLC 3.5 51.8 - - + -
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Residues in contact with VAL 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C VAL* 3.0 35.2 + - + +
18C LEU* 3.2 21.3 - - + +
20C PHE* 1.3 86.5 - - + +
22C LEU* 1.3 72.4 + - + +
24C GLN* 2.9 6.3 + - - +
25C VAL* 2.8 44.1 + - + +
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C LEU* 3.0 32.7 + - + +
19C VAL* 4.0 2.5 - - - +
21C VAL* 1.3 84.7 - - + +
23C ASP* 1.3 53.2 + - - +
25C VAL* 3.9 11.7 - - + +
26C SER* 2.6 39.0 + - - -
141C LEU* 3.8 7.0 - - + -
204C OLC 3.9 46.1 - - + +
301F OLC 4.2 17.9 - - + -
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Residues in contact with ASP 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C VAL* 2.9 21.7 + - + +
20C PHE* 3.2 7.0 - - - +
21C VAL 3.1 0.2 - - - -
22C LEU* 1.3 77.4 - - - +
24C GLN* 1.3 63.1 + - - +
26C SER* 3.4 3.5 - - - -
27C LYS* 2.6 65.9 + - - +
107C GLY 5.6 0.4 - - - +
111C GLY* 3.4 17.8 - - - -
140C ASN* 4.2 0.2 - - - +
141C LEU* 3.7 18.0 + - + +
142C ALA* 2.9 33.9 + - + +
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Residues in contact with GLN 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 3.0 30.0 + - + +
21C VAL* 2.9 9.7 + - - +
23C ASP* 1.3 84.0 + - - +
25C VAL* 1.3 60.6 + - + +
27C LYS* 3.5 8.0 + - - +
28C ALA* 3.0 30.0 + - - +
111C GLY* 3.0 32.1 + - - -
114C TYR* 3.3 37.8 - - + +
115C ASP* 3.6 11.1 + - - +
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Residues in contact with VAL 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C VAL* 2.8 29.7 + - + +
22C LEU* 3.9 15.0 - - + +
24C GLN* 1.3 70.8 - - + +
26C SER* 1.3 64.6 + - - +
28C ALA* 3.5 5.4 + - - +
29C PHE* 3.1 24.1 + - + +
204C OLC 5.9 4.9 - - + -
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Residues in contact with SER 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU 2.6 22.8 + - - -
23C ASP* 3.4 7.0 - - - -
25C VAL* 1.3 76.0 - - - +
27C LYS* 1.3 64.4 + - - +
29C PHE* 3.2 13.9 + - - +
30C PHE* 3.2 25.0 + - - -
125C PHE* 3.5 24.9 - - - -
141C LEU* 3.3 20.5 - - - +
204C OLC 4.5 13.2 - - - +
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Residues in contact with LYS 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 ASP* 2.6 48.2 + - - +
24C GLN* 3.9 11.2 - - - +
26C SER* 1.3 78.7 - - - +
28C ALA* 1.3 53.2 - - - +
30C PHE* 3.2 2.5 + - - +
31C GLN* 2.7 40.6 + - + +
111C GLY 3.6 2.8 + - - -
112C ASN* 3.1 19.8 + - - -
115C ASP* 2.5 40.5 + - - +
123C VAL* 3.6 28.0 - - + +
125C PHE* 4.1 14.6 - - + -
140C ASN* 3.2 20.2 - - - +
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Residues in contact with ALA 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN 3.0 19.8 + - - +
25C VAL* 3.8 6.5 - - - +
27C LYS* 1.3 75.1 - - - +
29C PHE* 1.3 63.2 + - - +
31C GLN* 3.3 11.0 + - - +
32C ALA* 3.1 22.7 + - - +
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Residues in contact with PHE 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C VAL* 3.1 15.6 + - + +
26C SER* 3.3 10.1 - - - +
28C ALA* 1.3 76.2 - - - +
30C PHE* 1.3 84.1 + + + +
32C ALA* 3.0 21.2 + - + +
33C GLU* 3.0 33.7 + - + +
204C OLC 3.5 51.4 - - + -
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Residues in contact with PHE 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C SER* 3.2 25.9 + - - +
27C LYS* 4.1 2.2 - - - +
29C PHE* 1.3 99.9 - + - +
31C GLN* 1.3 64.7 + - - +
32C ALA 3.1 1.3 - - - -
33C GLU* 3.8 4.5 - - + +
34C LEU* 3.2 48.2 + - + +
40C ILE* 5.7 0.4 - - + -
49C TRP* 3.5 51.4 - + + -
50C THR 4.5 1.1 - - - +
51C LEU* 3.5 11.9 - - + +
125C PHE* 3.5 46.9 - + + -
204C OLC 4.2 21.8 - - + -
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Residues in contact with GLN 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 LYS* 2.7 28.3 + - + +
28C ALA* 3.3 11.2 - - - +
30C PHE* 1.3 76.8 - - - +
32C ALA* 1.3 58.3 + - - +
34C LEU 3.9 9.4 - - - +
51C LEU* 3.4 9.1 - - - +
53C TYR* 2.6 47.0 + - - -
119C LEU* 5.6 6.3 - - + +
121C HIS* 5.9 0.2 - - - -
123C VAL* 3.2 25.5 - - + +
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Residues in contact with ALA 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ALA 3.1 10.1 + - - +
29C PHE* 3.0 12.1 + - + +
31C GLN* 1.3 80.0 - - - +
33C GLU* 1.3 67.6 + - - +
34C LEU 3.5 0.6 - - - +
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Residues in contact with GLU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C PHE* 3.0 38.7 + - + +
30C PHE* 3.6 5.1 + - + -
31C GLN 3.6 0.2 - - - -
32C ALA* 1.3 84.0 - - - +
34C LEU* 1.3 69.4 + - + +
38C GLN* 4.5 4.2 + - - +
40C ILE* 5.0 3.3 - - + +
204C OLC 4.0 28.7 + - - +
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PHE* 3.2 37.1 + - + +
31C GLN 3.9 7.4 - - - +
32C ALA 3.5 1.3 - - - +
33C GLU* 1.3 85.5 - - + +
35C SER* 1.3 60.8 + - - +
38C GLN* 3.5 31.9 - - + +
40C ILE* 3.5 30.7 - - + -
49C TRP* 4.4 5.2 - - + -
50C THR* 3.3 37.7 - - - +
51C LEU* 3.2 25.6 - - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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