Contacts of the helix formed by residues 19 - 39 (chain C) in PDB entry 2X1L
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 HIS 19 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C VAL* 4.3 10.5 - - + +
18C PRO* 1.3 76.2 - - - +
20C ILE* 1.3 68.2 + - + +
21C GLY* 3.4 10.4 + - - -
22C HIS* 3.2 42.7 + + - +
23C ALA 3.3 9.0 + - - -
81C LEU* 5.0 0.2 - - - +
310C VAL* 3.6 20.6 - - + +
312C PRO* 3.7 9.8 - - - +
601C ADN 3.1 40.2 + + - -
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Residues in contact with ILE 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C HIS* 1.3 79.3 - - + +
21C GLY* 1.3 58.6 + - - +
23C ALA* 3.3 10.1 + - + +
24C TYR* 2.8 28.6 + - - +
295C LEU* 3.8 32.3 - - + +
296C LEU* 5.5 1.1 - - - -
310C VAL* 3.1 21.0 + - + +
312C PRO* 4.5 7.0 - - + -
315C LEU* 3.7 26.0 - - + -
324C VAL* 5.1 3.1 - - + -
328C LEU* 4.0 26.5 - - + -
340C TYR* 3.5 34.3 - - + +
601C ADN 5.3 1.1 - - - +
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Residues in contact with GLY 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C HIS* 3.2 5.4 + - - -
20C ILE* 1.3 79.7 - - - +
22C HIS* 1.3 65.5 + - - +
24C TYR* 3.5 6.8 - - - +
25C GLU* 3.3 19.6 + - - +
295C LEU* 5.0 1.3 - - - -
601C ADN 3.5 52.1 + - - -
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Residues in contact with HIS 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA* 3.9 19.4 - - + +
13C TYR 5.1 3.1 + - - -
17C VAL 4.6 1.6 - - - -
18C PRO* 3.7 7.1 - - + +
19C HIS* 3.2 59.3 + + - +
21C GLY* 1.3 73.7 - - - +
23C ALA* 1.3 65.0 + - - +
25C GLU* 3.2 5.7 + - - +
26C TYR* 3.1 47.1 + - + -
78C PHE* 3.9 19.3 - + + -
81C LEU* 5.0 0.2 - - + -
601C ADN 3.6 38.1 - + - -
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Residues in contact with ALA 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C HIS 3.3 3.8 + - - +
20C ILE* 3.3 13.4 + - + +
22C HIS* 1.3 77.7 - - - +
24C TYR* 1.3 61.7 + - - +
26C TYR* 3.3 2.9 + - - +
27C ILE* 3.0 35.6 + - + +
81C LEU* 4.7 2.1 - - + +
85C LEU* 3.8 26.2 - - + -
312C PRO* 3.7 30.7 - - + -
324C VAL* 6.4 0.7 - - + -
328C LEU* 4.6 0.9 - - + -
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Residues in contact with TYR 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ILE 2.8 18.8 + - - +
21C GLY* 3.5 6.5 - - - +
23C ALA* 1.3 75.7 - - - +
25C GLU* 1.3 61.4 + - - +
27C ILE* 4.1 1.8 - - - +
28C ALA* 3.1 25.9 + - - +
292C HIS* 3.8 34.3 - + - +
293C GLY 3.8 10.7 + - - -
294C TRP 5.5 0.2 - - - -
295C LEU* 4.2 30.7 - - + -
328C LEU* 3.2 47.7 - - + +
329C LEU* 4.7 4.7 - - + -
332C VAL* 4.2 26.7 + - + +
334C PHE* 3.3 33.2 - + - -
335C GLY 4.9 1.0 + - - -
336C GLN 4.9 2.1 + - - -
601C ADN 4.4 2.9 - + - -
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Residues in contact with GLU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C THR* 3.6 8.3 - - - -
10C ALA* 3.0 36.6 + - - +
21C GLY 3.3 6.4 + - - +
22C HIS* 3.2 9.2 + - - +
24C TYR* 1.3 80.0 - - - +
26C TYR* 1.3 59.0 + - + +
28C ALA* 3.8 3.9 - - - +
29C THR* 2.7 43.5 + - - +
261C MET* 3.9 14.0 - - + +
263C GLY 3.5 1.9 + - - -
292C HIS* 2.7 41.5 + - + +
601C ADN 2.9 31.1 + - - +
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Residues in contact with TYR 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C THR* 4.0 14.4 - - + -
10C ALA 4.4 6.5 + - - -
12C ALA* 3.7 25.8 + - - +
22C HIS* 3.1 37.2 + + + +
23C ALA* 3.9 8.3 - - - +
25C GLU* 1.3 80.3 - - + +
27C ILE* 1.3 58.9 + - - +
29C THR* 3.4 1.2 + - - -
30C ASP* 2.8 27.9 + - - +
45C TYR* 3.1 13.1 + - - +
47C THR* 3.9 12.3 - - - -
48C GLY 4.4 4.9 + - - -
78C PHE* 3.8 14.3 - + - -
81C LEU* 4.6 8.3 - - + -
82C GLN* 3.4 45.2 + - + +
85C LEU* 4.5 6.7 - - + -
87C ILE* 3.6 17.4 - - + +
601C ADN 5.4 2.1 + - - -
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Residues in contact with ILE 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ALA* 3.0 23.7 + - + +
24C TYR* 4.1 3.1 - - - +
26C TYR* 1.3 72.5 - - - +
28C ALA* 1.3 61.3 + - - +
30C ASP* 3.3 3.2 + - - +
31C ALA* 2.9 28.6 + - - +
85C LEU* 4.3 22.2 - - + -
87C ILE* 4.1 16.4 - - + -
324C VAL* 4.7 4.0 - - + -
325C ARG* 3.8 60.4 + - + +
328C LEU* 3.7 24.7 - - + -
329C LEU* 4.2 13.9 - - + -
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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 TYR 3.1 18.7 + - - +
25C GLU* 3.8 4.7 - - - +
27C ILE* 1.3 78.3 - - - +
29C THR* 1.3 61.0 + - - +
31C ALA* 3.4 4.1 + - - +
32C ILE* 3.4 25.8 + - - +
261C MET* 4.0 3.4 - - + -
329C LEU* 3.7 19.9 - - + +
334C PHE* 3.5 37.0 - - + -
409C MET* 3.9 4.4 - - + +
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Residues in contact with THR 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 3.7 27.8 - - + -
8C THR 4.0 2.2 - - - +
9C THR* 3.5 23.5 - - + +
25C GLU* 2.7 23.5 + - - +
28C ALA* 1.3 73.2 - - - +
30C ASP* 1.3 64.9 + - - +
32C ILE* 3.3 5.5 + - - +
33C ALA* 3.0 22.2 + - - +
45C TYR* 3.5 22.0 - - + -
261C MET* 3.4 29.4 - - + +
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Residues in contact with ASP 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TYR 2.8 18.4 + - - +
27C ILE 3.3 5.6 + - - +
29C THR* 1.3 77.8 - - - +
31C ALA* 1.3 56.1 + - - +
33C ALA 3.8 0.3 - - - -
34C ARG* 2.8 47.6 + - - +
45C TYR* 3.2 11.7 + - - +
86C ASN 3.3 1.6 - - - +
87C ILE* 3.8 13.7 - - + -
88C SER* 2.7 44.2 + - - -
325C ARG* 2.8 31.7 + - - +
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Residues in contact with ALA 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ILE 2.9 16.7 + - - +
28C ALA 3.6 7.0 - - - +
29C THR 3.3 0.2 - - - -
30C ASP* 1.3 76.4 - - - +
32C ILE* 1.3 57.0 + - - +
35C PHE* 3.0 24.8 + - - +
325C ARG* 5.0 0.7 - - - +
329C LEU* 3.8 22.7 - - + -
404C PHE* 3.4 15.3 - - + -
409C MET* 4.5 2.2 - - + -
467C PRO* 3.2 34.5 + - - +
468C VAL* 4.7 0.7 - - + -
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Residues in contact with ILE 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PHE* 4.0 16.8 - - + -
7C ILE* 3.8 16.2 - - + -
28C ALA 3.4 8.9 + - - +
29C THR 3.3 5.1 + - - +
30C ASP 3.3 0.2 - - - -
31C ALA* 1.3 74.2 - - - +
33C ALA* 1.3 65.7 + - - +
35C PHE* 3.2 2.8 + - + +
36C LYS* 3.0 30.1 + - + +
259C LEU* 4.1 7.2 - - + -
261C MET* 3.6 33.4 - - + -
404C PHE* 4.1 22.9 - - + +
407C PRO* 3.6 28.0 - - + -
409C MET* 3.9 15.5 - - - -
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Residues in contact with ALA 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PHE* 4.9 0.9 - - - -
7C ILE* 4.0 17.6 - - + +
29C THR 3.0 13.2 + - - +
30C ASP 3.8 2.5 - - - +
32C ILE* 1.3 75.7 - - - +
34C ARG* 1.3 61.8 + - - +
36C LYS* 3.4 5.5 + - - +
37C ARG* 3.1 36.3 + - - +
43C VAL* 3.9 12.1 - - + +
45C TYR* 3.5 32.5 - - + -
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Residues in contact with ARG 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ASP* 2.8 40.7 + - - +
33C ALA* 1.3 70.2 - - - +
35C PHE* 1.3 65.7 + - - +
37C ARG* 3.5 10.6 + - - +
38C LEU* 3.1 32.3 + - + +
86C ASN* 2.8 41.4 + - - +
88C SER* 3.7 27.5 - - - +
466C GLN 4.3 1.7 + - - +
467C PRO* 3.7 30.5 - - + -
470C PRO* 3.7 26.6 - - - +
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Residues in contact with PHE 35 (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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31C ALA 3.0 18.8 + - - +
32C ILE* 3.5 5.4 - - + +
34C ARG* 1.3 77.0 - - - +
36C LYS* 1.3 68.8 + - + +
38C LEU 3.2 1.4 + - - -
39C ASP* 2.9 44.8 + - + +
397C LEU* 4.8 5.8 - - + -
400C VAL* 3.5 24.5 - - + -
401C ARG* 3.6 35.7 - - + -
404C PHE* 3.7 35.0 - + + -
405C ASP* 6.1 0.4 - - - -
464C LEU* 4.9 3.8 - - + -
467C PRO* 3.8 12.1 - - + +
489C PHE* 3.3 36.7 - + - -
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Residues in contact with LYS 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PHE* 3.7 44.3 - - + -
32C ILE* 3.0 26.8 + - + +
33C ALA 3.8 0.9 - - - +
34C ARG 3.3 0.2 - - - -
35C PHE* 1.3 82.1 - - + +
37C ARG* 1.3 62.4 + - - +
39C ASP* 3.2 3.5 + - - +
40C GLY 3.2 5.7 + - - -
41C TYR* 2.8 70.0 + - + +
43C VAL* 3.6 19.3 - - + -
401C ARG* 5.9 2.2 - - - +
404C PHE* 5.4 3.6 - - - -
405C ASP* 2.8 31.9 + - - -
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Residues in contact with ARG 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ALA* 3.1 29.1 + - - +
34C ARG* 3.7 12.0 - - - +
36C LYS* 1.3 76.6 - - - +
38C LEU* 1.3 62.6 + - + +
40C GLY* 3.4 12.3 + - - -
41C TYR 4.0 11.5 + - - +
43C VAL* 3.7 28.7 + - + +
45C TYR* 3.9 10.1 - - - +
88C SER* 2.8 51.4 + - - -
90C ASP* 3.5 24.4 + - - -
488C ASP* 4.3 6.8 - - - +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ARG* 3.1 23.6 + - + +
37C ARG* 1.3 77.3 - - + +
39C ASP* 1.3 58.0 + - - +
40C GLY 3.3 2.1 + - - -
466C GLN* 3.8 32.5 - - + +
467C PRO* 3.8 8.5 - - + -
487C ARG* 3.4 24.7 - - + +
488C ASP* 3.6 21.9 - - - +
489C PHE* 3.0 62.0 + - + +
490C SER 4.7 0.5 + - - -
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Residues in contact with ASP 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 2.9 25.3 + - + +
36C LYS* 3.2 7.1 + - - +
37C ARG 3.2 0.6 - - - -
38C LEU* 1.3 76.9 - - - +
40C GLY* 1.3 58.1 + - - +
41C TYR* 3.7 24.1 + - + -
401C ARG* 2.8 52.8 + - - +
489C PHE* 3.8 16.8 - - + +
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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