Contacts of the helix formed by residues 17 - 35 (chain L) in PDB entry 1IJ4
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 GLN 17 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I PRO 3.8 14.7 - - - +
37I LEU* 3.5 19.7 + - - +
38I PRO* 3.3 33.9 - - - +
16L LEU* 1.3 73.3 - - - +
18L PRO* 1.4 73.7 - - + +
19L ASP* 4.4 4.7 - - + +
20L GLU* 2.9 46.3 + - + +
21L PHE* 3.1 22.7 + - - +
75L HIS* 4.4 2.0 - - - -
137L LYS* 4.2 5.4 - - - +
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Residues in contact with PRO 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I PRO* 3.9 15.7 - - + +
16L LEU 4.5 1.3 - - - +
17L GLN* 1.4 86.7 - - + +
19L ASP* 1.3 56.5 + - - +
21L PHE* 3.6 2.1 + - + +
22L GLN* 3.1 30.4 + - - +
75L HIS* 4.8 11.1 - - - +
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Residues in contact with ASP 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L GLN* 3.5 4.3 - - + +
18L PRO* 1.3 75.5 - - - +
20L GLU* 1.3 60.7 + - - +
22L GLN* 4.4 8.5 - - - +
23L LYS* 2.7 63.2 + - - +
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Residues in contact with GLU 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L LEU* 3.5 10.6 - - + -
17L GLN* 2.9 52.7 + - + +
19L ASP* 1.3 72.8 - - - +
21L PHE* 1.4 64.9 + - - +
23L LYS* 3.3 15.1 + - - +
24L ILE* 3.3 15.3 + - - +
113L ASP* 3.8 7.1 - - - +
135L ILE* 4.0 35.2 - - + +
136L GLY* 6.3 0.4 - - - -
137L LYS* 2.7 43.5 + - - +
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Residues in contact with PHE 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L PHE* 4.0 25.8 - + - -
11L ASP 3.4 26.9 - - - -
12L GLY* 4.0 2.2 - - - -
16L LEU* 4.3 6.5 - - + +
17L GLN 3.1 11.5 + - - +
18L PRO 4.1 3.1 - - - +
20L GLU* 1.4 74.2 - - - +
22L GLN* 1.3 62.0 + - - +
24L ILE* 3.2 16.2 + - + +
25L LEU* 3.1 44.8 + - + +
46L GLN* 3.5 29.4 - - - -
73L VAL* 4.7 0.4 - - + -
74L LYS* 3.5 21.1 - - - -
75L HIS* 3.7 39.3 - + + +
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Residues in contact with GLN 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L PRO 3.1 18.7 + - - +
19L ASP* 4.7 9.0 - - - +
21L PHE* 1.3 75.1 - - - +
23L LYS* 1.4 56.9 + - - +
25L LEU* 3.3 28.1 + - - +
26L ASP* 2.9 63.8 + - - +
29L LYS* 3.6 13.1 - - - +
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Residues in contact with LYS 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L ASP* 2.7 55.5 + - - +
20L GLU* 3.3 10.5 + - - +
22L GLN* 1.4 71.6 - - - +
24L ILE* 1.4 58.7 + - - +
26L ASP* 4.2 8.0 - - - +
27L PHE* 3.0 32.2 + - - +
135L ILE* 4.5 7.0 - - + -
163L LEU* 3.8 18.9 - - + +
164L ASP* 3.8 21.1 - - - +
166L PHE* 4.1 26.7 - - + -
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Residues in contact with ILE 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L PHE* 3.6 27.6 - - + -
11L ASP 4.4 3.1 - - - +
16L LEU* 3.5 32.1 - - + -
20L GLU 3.3 11.0 + - - +
21L PHE* 3.2 19.5 + - + +
23L LYS* 1.4 71.6 - - - +
25L LEU* 1.3 58.9 + - + +
27L PHE* 3.9 1.2 - - - +
28L MET* 3.0 44.7 + - + +
111L ILE* 3.7 47.6 - - + +
135L ILE* 3.9 11.4 - - + -
163L LEU* 4.0 5.5 - - - +
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Residues in contact with LEU 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L PHE* 3.1 34.0 + - + +
22L GLN* 3.3 35.2 + - + +
24L ILE* 1.3 74.3 - - - +
26L ASP* 1.3 56.1 + - - +
28L MET* 3.7 17.0 + - + -
29L LYS* 3.1 41.4 + - - +
70L LEU* 3.8 15.3 - - + +
73L VAL* 3.7 51.1 - - + +
74L LYS* 5.3 3.6 - - + +
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Residues in contact with ASP 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L GLN* 2.9 43.6 + - - +
23L LYS* 4.2 7.3 + - - +
25L LEU* 1.3 67.9 - - - +
27L PHE* 1.3 64.1 + - - +
29L LYS* 2.7 34.9 + - - +
30L ASP* 3.3 27.4 + - - +
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Residues in contact with PHE 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L PHE* 5.7 1.3 - + - -
23L LYS 3.0 22.2 + - - +
24L ILE 3.9 3.4 - - - +
26L ASP* 1.3 72.3 - - - +
28L MET* 1.3 64.8 + - + +
30L ASP* 4.1 0.6 - - - -
31L VAL* 3.2 44.4 + - + +
109L ILE* 4.8 12.1 - - + -
111L ILE* 4.7 10.8 - - + -
133L ILE* 3.9 40.6 - - + -
163L LEU* 4.1 28.3 - - + -
168L LYS* 4.1 22.7 - - - -
169L LEU* 3.7 32.0 - - + +
172L LEU* 4.1 10.5 - - + -
173L PHE* 4.4 1.3 - + - -
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Residues in contact with MET 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L PHE* 3.6 46.0 - - + -
10L PHE* 3.3 52.3 - - + -
24L ILE* 3.0 36.5 + - + +
25L LEU* 4.0 23.3 - - + -
27L PHE* 1.3 73.4 - - + +
29L LYS* 1.4 61.8 + - - +
32L MET* 3.2 27.5 + - - +
44L ALA* 5.4 0.9 - - - -
70L LEU* 3.6 20.6 - - + -
111L ILE* 4.6 5.8 - - + -
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Residues in contact with LYS 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L GLN* 3.6 13.5 - - - +
25L LEU* 3.1 33.1 + - - +
26L ASP* 2.7 32.6 + - - +
27L PHE 3.5 0.2 - - - -
28L MET* 1.4 76.8 - - - +
30L ASP* 1.3 69.5 + - - +
32L MET 3.5 0.5 + - - -
33L LYS* 3.2 29.0 + - - +
66L PRO* 3.4 37.4 - - - +
67L ASP* 4.4 17.5 - - - +
70L LEU* 3.5 26.6 - - + +
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Residues in contact with ASP 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L ASP* 3.3 14.3 + - - +
27L PHE* 4.8 0.4 - - - +
29L LYS* 1.3 79.8 - - - +
31L VAL* 1.4 59.5 + - - +
32L MET 3.5 0.4 - - - -
33L LYS* 2.7 45.8 + - + +
34L LYS* 3.0 29.3 + - - +
169L LEU* 4.3 21.6 - - + +
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Residues in contact with VAL 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L PHE* 3.7 27.1 - - + -
27L PHE* 3.2 34.4 + - + +
28L MET 4.2 0.2 - - - +
30L ASP* 1.4 75.3 - - - +
32L MET* 1.3 56.9 + - - +
34L LYS* 3.5 5.5 + - - +
35L LEU* 3.1 28.6 + - - +
42L PHE* 4.2 8.5 - - + -
109L ILE* 4.9 0.2 - - + -
169L LEU* 3.5 17.6 - - + +
173L PHE* 3.4 52.4 - - + -
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Residues in contact with MET 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L PHE* 3.7 20.2 - - + -
28L MET 3.2 20.4 + - - +
29L LYS 3.5 2.1 + - - +
30L ASP 3.5 0.2 - - - -
31L VAL* 1.3 75.0 - - - +
33L LYS* 1.3 55.8 + - - +
35L LEU 3.5 1.1 - - - -
36L SER* 3.1 28.9 + - - -
42L PHE* 3.8 35.4 - - + -
55L PHE* 3.7 33.2 - - + -
60L TYR* 3.7 18.8 + - + -
66L PRO* 3.5 38.6 - - + +
70L LEU* 3.8 17.7 - - + -
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Residues in contact with LYS 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L LYS* 3.2 25.8 + - - +
30L ASP* 2.7 46.0 + - + +
31L VAL 3.4 0.6 - - - -
32L MET* 1.3 72.8 - - - +
34L LYS* 1.3 62.8 + - - +
36L SER* 3.2 23.1 + - - -
66L PRO* 3.6 18.4 - - + -
67L ASP* 3.3 30.1 + - - -
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Residues in contact with LYS 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L ASP 3.0 18.7 + - - +
31L VAL* 3.7 6.5 - - - +
33L LYS* 1.3 74.5 - - - +
35L LEU* 1.3 60.5 + - - +
36L SER 3.7 0.6 + - - -
38L THR* 5.1 2.3 - - - +
169L LEU* 4.1 22.7 - - + +
170L LYS* 5.7 2.0 - - - +
173L PHE* 2.8 45.1 + - + +
174L THR* 4.4 7.2 + - - +
177L GLN* 2.9 20.2 + - - -
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Residues in contact with LEU 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L VAL 3.1 13.0 + - - +
32L MET 3.5 4.7 - - - -
34L LYS* 1.3 84.9 - - - +
36L SER* 1.3 58.5 + - - +
37L ASN 3.5 1.9 + - - -
38L THR* 2.8 35.9 + - + +
40L TYR* 3.7 50.6 - - + +
42L PHE* 4.1 20.9 - - + -
60L TYR* 4.0 6.1 + - - -
173L PHE* 3.8 33.4 - - + +
177L GLN* 3.5 29.2 - - + +
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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
------------------------------------------------------------
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