Contacts of the helix formed by residues 3 - 19 (chain L) in PDB entry 4B86
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 PRO 3 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2L ASN* 1.3 86.2 - - + +
4L VAL* 1.3 53.6 + - - +
5L ASN 3.6 1.8 - - - -
6L ALA* 3.8 17.7 - - + -
7L THR* 2.7 34.0 + - - +
63L GLN* 3.8 0.4 - - - +
65L TYR* 3.4 22.7 - - - +
93L ASN* 3.9 20.9 - - - +
95L GLN* 3.6 13.0 - - + +
96L LEU* 3.7 20.6 - - + +
99L LEU* 3.7 20.0 - - + -
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Residues in contact with VAL 4 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237I GLN* 3.8 15.0 - - + +
241I GLN* 3.4 32.3 - - + +
2L ASN* 3.2 24.5 - - - +
3L PRO* 1.3 70.1 - - - +
5L ASN* 1.3 65.0 + - - +
7L THR* 3.0 5.1 + - - -
8L ALA* 2.9 32.8 + - + +
61L THR* 6.1 4.9 - - + -
63L GLN* 3.1 17.5 + - - +
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Residues in contact with ASN 5 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4L VAL* 1.3 78.4 - - - +
6L ALA* 1.3 58.5 + - - +
8L ALA* 3.7 5.0 - - - +
9L LEU* 2.9 45.5 + - + +
41L SER* 5.1 5.2 - - - -
63L GLN* 3.0 36.9 + - - +
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Residues in contact with ALA 6 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L PRO* 3.7 15.1 + - + -
4L VAL 3.3 0.6 - - - -
5L ASN* 1.3 79.5 - - - +
7L THR* 1.3 57.4 + - - +
9L LEU* 3.4 0.3 + - - +
10L TYR* 2.9 28.8 + - - +
38L PHE* 3.6 6.6 - - - -
41L SER* 3.8 22.5 + - - +
42L LEU* 3.8 28.0 - - + -
63L GLN* 4.4 1.0 + - - -
65L TYR* 5.3 2.2 - - + -
96L LEU* 4.8 1.1 - - + -
99L LEU* 3.8 13.2 - - + +
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Residues in contact with THR 7 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233I ILE* 5.3 1.8 - - + -
237I GLN* 3.5 25.7 + - + +
232J LEU* 4.9 7.9 - - + -
236J GLN* 5.2 1.1 - - - +
3L PRO 2.7 20.6 + - - +
4L VAL* 3.0 15.6 + - - -
6L ALA* 1.3 73.5 - - - +
8L ALA* 1.3 63.1 + - - +
10L TYR* 3.2 7.2 + - + +
11L ILE* 3.0 32.6 + - - +
95L GLN* 3.4 29.6 - - + +
99L LEU* 3.5 24.0 - - + -
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Residues in contact with ALA 8 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237I GLN* 6.0 0.2 - - - +
4L VAL* 2.9 20.3 + - + +
5L ASN* 3.7 5.8 - - - +
7L THR* 1.3 75.7 + - - +
9L LEU* 1.3 57.6 + - + +
11L ILE* 3.1 14.2 + - - +
12L SER* 2.9 31.6 + - - +
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Residues in contact with LEU 9 (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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37C TYR* 5.9 0.7 - - - +
5L ASN* 2.9 27.0 + - + +
6L ALA 3.6 4.5 - - - +
8L ALA* 1.3 75.1 - - + +
10L TYR* 1.3 60.3 + - - +
12L SER* 3.8 5.4 - - - -
13L ALA* 2.9 32.9 + - - +
34L LEU* 4.1 23.8 - - + +
37L TYR* 3.8 16.6 - - + +
38L PHE* 3.6 33.3 - - + +
41L SER* 3.5 26.9 - - - +
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Residues in contact with TYR 10 (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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230I LEU* 3.6 13.2 - - + -
233I ILE* 5.2 0.7 - - + -
225J ILE* 3.7 12.5 - - - +
229J GLN* 2.9 43.1 + - + +
232J LEU* 4.7 10.3 - - + -
6L ALA 2.9 17.1 + - - +
7L THR* 3.2 6.3 + - - +
9L LEU* 1.3 75.0 - - - +
11L ILE* 1.3 60.7 + - + +
13L ALA* 4.7 0.2 - - - -
14L SER* 2.9 55.1 + - - -
38L PHE* 3.5 32.9 - + + -
99L LEU* 4.1 18.2 - - + -
102L CYS* 3.4 42.7 - - + -
106L LEU* 4.8 4.3 - - + -
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Residues in contact with ILE 11 (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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230I LEU* 3.7 28.0 - - + +
233I ILE* 4.1 14.1 - - + -
234I GLU* 4.0 37.7 - - + +
237I GLN* 5.0 4.7 - - + -
7L THR* 3.0 25.5 + - - +
8L ALA* 3.4 11.0 - - - +
10L TYR* 1.3 77.5 - - + +
12L SER* 1.3 57.9 + - - +
15L ARG* 2.9 72.4 + - - +
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Residues in contact with SER 12 (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 ALA* 2.9 18.5 + - - +
9L LEU* 3.8 6.5 - - - -
10L TYR 3.3 0.2 - - - -
11L ILE* 1.3 77.1 - - - +
13L ALA* 1.3 57.6 + - - +
15L ARG* 3.2 5.8 + - - +
16L LEU* 2.9 38.8 + - - +
34L LEU* 3.5 24.9 - - - +
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Residues in contact with ALA 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L LEU 2.9 21.7 + - - +
10L TYR 4.1 1.6 - - - +
12L SER* 1.3 73.4 - - - +
14L SER* 1.3 58.1 + - - +
16L LEU* 3.4 4.3 + - - +
17L VAL* 2.9 34.1 + - - +
31L ILE* 5.4 1.3 - - - +
34L LEU* 3.5 15.8 - - + +
35L LEU* 3.9 25.6 - - + -
38L PHE* 4.2 17.0 - - + -
106L LEU* 4.2 5.6 - - + -
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Residues in contact with SER 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226I LEU* 6.0 0.3 - - - +
230I LEU* 3.5 20.4 - - - -
225J ILE* 4.6 1.9 - - - +
229J GLN* 4.7 1.3 + - - -
10L TYR* 2.9 48.6 + - - -
13L ALA* 1.3 76.1 - - - +
15L ARG* 1.3 58.0 + - - +
17L VAL* 3.3 1.0 + - - +
18L LEU* 2.9 40.0 + - - +
106L LEU* 3.5 23.6 - - - +
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Residues in contact with ARG 15 (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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227I LEU* 4.3 16.6 + - + -
230I LEU* 3.6 18.3 + - + +
231I ASP* 3.0 46.0 + - - +
234I GLU* 2.6 32.5 + - - -
11L ILE* 2.9 40.8 + - - +
12L SER* 3.6 5.6 - - - +
14L SER* 1.3 75.6 - - - +
16L LEU* 1.3 65.5 + - + +
18L LEU 3.7 0.5 + - - -
19L ASN* 3.2 34.8 + - - +
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Residues in contact with LEU 16 (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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12L SER* 2.9 30.3 + - - +
13L ALA* 3.6 5.2 - - - +
15L ARG* 1.3 80.6 - - + +
17L VAL* 1.3 61.3 + - - +
19L ASN* 3.6 3.8 + - - +
20L TYR* 3.5 14.7 + - - -
27L ALA* 5.4 4.7 - - + +
30L GLU* 3.4 42.6 - - + +
31L ILE* 3.7 36.1 - - + +
34L LEU* 3.8 24.0 - - + -
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Residues in contact with VAL 17 (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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13L ALA 2.9 22.6 + - - +
14L SER 3.8 3.6 - - - +
16L LEU* 1.3 77.1 - - - +
18L LEU* 1.3 62.8 + - + +
20L TYR* 3.3 20.7 - - + +
31L ILE* 3.9 29.2 - - + -
35L LEU* 5.0 1.8 - - + -
106L LEU* 3.9 21.1 - - + -
109L TYR* 3.9 31.8 - - + -
110L ILE* 3.9 28.3 - - + -
113L THR* 5.9 1.1 - - - +
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Residues in contact with LEU 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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223I LYS* 3.7 47.6 - - + +
226I LEU* 3.6 40.6 - - + -
227I LEU* 3.8 34.8 - - + +
230I LEU* 4.6 7.4 - - + -
222J LEU* 4.5 6.1 - - + -
14L SER* 2.9 29.8 + - - +
15L ARG 4.2 0.2 - - - +
17L VAL* 1.3 78.9 - - + +
19L ASN* 1.3 62.7 + - - +
20L TYR 3.3 3.2 + - - +
106L LEU* 5.8 2.9 - - + -
109L TYR* 5.0 9.4 - - + -
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Residues in contact with ASN 19 (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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227I LEU* 3.6 28.0 - - - +
15L ARG* 3.2 22.9 + - - +
16L LEU* 3.6 5.4 + - - +
17L VAL 3.3 0.4 - - - -
18L LEU* 1.3 80.7 - - - +
20L TYR* 1.3 63.6 + - - +
21L ASP* 3.5 5.4 + - - +
27L ALA* 5.7 2.6 - - - +
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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
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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