Contacts of the helix formed by residues 11 - 32 (chain A) in PDB entry 4M8J
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 GLU 11 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 1.3 74.5 - - - +
12A PRO* 1.3 56.8 - - - +
13A LYS* 3.0 37.1 + - + +
14A VAL* 2.9 15.8 + - + +
15A PHE* 2.8 33.6 + - - +
170A ARG* 4.4 14.2 + - - +
434A THR 3.2 20.6 + - - +
435A CYS* 3.5 12.3 - - - +
436A ARG* 3.3 38.7 + - - +
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Residues in contact with PRO 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.2 22.9 - - + +
11A GLU* 1.3 88.8 - - - +
13A LYS* 1.3 61.7 + - - +
14A VAL 3.2 0.8 + - - -
15A PHE* 3.8 6.1 - - + -
16A PHE* 3.5 47.0 + - + +
17A PRO* 3.8 5.2 - - - +
436A ARG* 5.4 4.5 - - - +
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Residues in contact with LYS 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 3.6 27.6 - - + +
12A PRO* 1.3 81.1 - - - +
14A VAL* 1.3 65.8 + - + +
17A PRO* 3.9 11.8 - - - +
170A ARG* 5.2 8.1 - - - +
172A SER* 5.6 1.2 + - - -
184A VAL 4.9 7.7 + - - -
185A ASN* 4.1 23.6 + - - +
186A GLY 4.3 2.8 + - - -
189A GLY 5.1 1.4 - - - -
190A THR* 3.1 53.9 + - + +
193A ASP* 5.1 4.2 + - - -
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Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 2.9 11.9 + - + +
13A LYS* 1.3 93.7 - - + +
15A PHE* 1.3 59.9 + - - +
16A PHE 3.7 0.4 - - - -
17A PRO* 4.2 2.2 - - - -
18A PRO* 3.2 26.6 - - - +
170A ARG* 3.8 25.8 - - - +
190A THR* 4.6 5.4 - - + -
193A ASP* 4.3 15.5 - - + +
194A ASN* 5.6 2.9 - - - +
197A LEU* 3.9 17.1 - - + +
433A SER 3.5 18.6 - - - +
434A THR* 3.3 28.7 - - - +
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Residues in contact with PHE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.8 24.9 - - + -
11A GLU 2.8 22.5 + - - +
12A PRO* 3.7 4.7 + - + -
14A VAL* 1.3 76.7 - - - +
16A PHE* 1.3 95.6 + + - +
18A PRO* 3.2 15.9 - - - +
19A LEU* 3.6 38.0 + - + +
434A THR* 3.4 29.2 - - + +
448A VAL* 3.6 29.4 - - + -
452A TRP* 4.2 11.0 - + - -
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Residues in contact with PHE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.2 14.1 - - + -
12A PRO* 3.5 41.8 + - + +
15A PHE* 1.3 102.4 - + - +
17A PRO* 1.4 74.2 - - + +
19A LEU* 3.3 7.9 + - + +
20A ILE* 3.0 38.0 + - + +
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Residues in contact with PRO 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PRO 3.8 11.7 - - - +
13A LYS 3.9 16.2 - - - +
14A VAL* 4.2 1.3 - - - -
15A PHE 3.8 0.9 - - - -
16A PHE* 1.4 93.6 - - + +
18A PRO* 1.4 72.1 - - + +
20A ILE* 3.1 9.6 + - + +
21A ILE* 3.1 33.8 + - + +
190A THR* 5.5 3.1 - - + -
194A ASN* 4.4 17.3 - - + -
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Residues in contact with PRO 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.2 19.7 - - - +
15A PHE 3.2 14.4 - - - +
17A PRO* 1.4 94.1 - - + +
19A LEU* 1.3 55.6 + - - +
21A ILE* 3.2 1.4 + - + +
22A VAL* 2.8 39.6 + - - +
194A ASN* 4.6 8.7 - - + +
197A LEU* 4.7 10.5 - - + -
198A VAL* 3.7 33.2 - - + +
201A ILE* 4.5 15.5 - - + -
452A TRP* 4.2 10.8 - - + -
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.6 37.5 - - + +
16A PHE* 3.3 12.5 + - + +
18A PRO* 1.3 80.7 - - - +
20A ILE* 1.3 62.8 + - + +
22A VAL* 4.7 3.0 - - - +
23A GLY* 3.2 18.2 + - - -
451A GLY 5.8 2.0 - - - +
452A TRP* 3.6 29.8 - - + -
455A LEU* 4.0 22.7 - - + +
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Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PHE* 3.0 31.3 + - + +
17A PRO* 3.4 9.2 - - + +
19A LEU* 1.3 74.5 - - + +
21A ILE* 1.3 64.9 + - + +
23A GLY* 3.1 3.5 + - - -
24A ILE* 2.8 51.0 + - + +
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Residues in contact with ILE 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PRO* 3.1 29.6 + - + +
18A PRO* 3.9 7.6 - - + +
20A ILE* 1.3 83.3 - - + +
22A VAL* 1.3 53.1 + - - +
24A ILE* 2.9 15.3 + - + +
25A LEU* 2.7 57.3 + - + +
194A ASN* 6.0 3.1 - - + -
195A PHE* 6.6 0.2 - - + -
198A VAL* 4.6 20.9 - - + -
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Residues in contact with VAL 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PRO 2.8 26.3 + - - +
19A LEU 4.7 0.7 - - - +
21A ILE* 1.3 73.6 - - + +
23A GLY* 1.3 61.2 + - - +
25A LEU* 4.1 7.8 - - + +
26A CYS* 3.3 21.5 + - - +
198A VAL* 4.4 21.8 - - + -
201A ILE* 4.1 21.3 - - + -
202A LEU* 4.9 6.1 - - + -
455A LEU* 3.6 29.8 - - + +
459A ILE* 3.5 33.4 - - + +
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Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU 3.2 14.5 + - - -
20A ILE 3.1 7.5 + - - -
21A ILE 3.1 0.6 - - - -
22A VAL* 1.3 78.0 - - - +
24A ILE* 1.3 61.7 + - - +
26A CYS* 3.4 8.8 + - - +
27A TRP* 3.1 21.5 + - - +
455A LEU* 5.0 5.8 - - - +
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Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 2.8 40.7 + - + +
21A ILE* 3.3 14.1 - - + +
23A GLY* 1.3 73.9 - - - +
25A LEU* 1.3 69.2 + - + +
27A TRP* 3.0 20.8 + - + +
28A LEU* 3.0 34.4 + - + +
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 2.7 43.4 + - + +
22A VAL* 4.1 9.0 - - + +
23A GLY 3.4 0.2 - - - -
24A ILE* 1.3 79.8 - - + +
26A CYS* 1.3 58.4 + - - +
28A LEU* 4.6 9.9 - - + +
29A THR* 3.0 30.1 + - - -
198A VAL* 5.2 4.7 - - + -
202A LEU* 5.0 22.9 - - + -
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Residues in contact with CYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL 3.3 12.8 + - - +
23A GLY* 3.5 11.4 - - - +
24A ILE 3.1 0.2 - - - -
25A LEU* 1.3 76.7 - - - +
27A TRP* 1.3 60.0 + - - +
29A THR* 4.6 0.7 - - - -
30A VAL* 2.7 49.4 + - - +
458A ILE* 4.2 16.4 - - + -
459A ILE* 6.0 3.1 - - + -
462A ILE* 3.6 30.7 - - + -
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Residues in contact with TRP 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLY 3.1 10.8 + - - +
24A ILE* 3.1 15.7 - - + +
26A CYS* 1.3 85.0 - - - +
28A LEU* 1.3 70.4 + - + +
30A VAL* 3.7 6.4 - - - +
31A ARG* 3.0 61.7 + - + +
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 3.0 30.3 + - + +
25A LEU* 4.6 11.4 - - + +
27A TRP* 1.3 85.5 - - + +
29A THR* 1.3 62.2 + - - +
31A ARG* 3.3 49.0 + - - +
32A ASP* 3.9 6.6 + - - +
36A SER* 4.3 2.8 + - - -
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Residues in contact with THR 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU 3.0 20.6 + - - -
26A CYS 3.2 2.5 + - - -
28A LEU* 1.3 76.4 - - - +
30A VAL* 1.3 62.2 + - - +
31A ARG 3.1 5.3 + - - -
32A ASP 3.4 8.3 + - - -
33A LEU* 3.4 8.7 - - - +
36A SER* 3.2 25.8 + - - +
462A ILE* 3.6 15.5 - - + -
466A LEU* 3.5 36.1 - - + -
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A CYS* 2.7 37.8 + - - +
27A TRP* 3.7 8.3 - - - +
29A THR* 1.3 75.4 - - - +
31A ARG* 1.3 63.4 + - - +
32A ASP 3.4 0.2 - - - -
33A LEU* 3.3 21.8 - - + +
462A ILE* 4.3 23.3 - - + +
465A ALA* 6.2 2.7 - - + -
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Residues in contact with ARG 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TRP* 3.0 57.5 + - + +
28A LEU* 3.3 38.3 + - - +
29A THR 3.1 1.0 - - - -
30A VAL* 1.3 82.0 - - + +
32A ASP* 1.3 64.4 + - + +
33A LEU* 4.9 0.2 - - - -
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Residues in contact with ASP 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU 3.9 5.0 + - - +
29A THR 3.4 4.0 + - - -
31A ARG* 1.3 87.6 - - + +
33A LEU* 1.3 59.5 + - - +
34A ASP* 3.1 24.5 + - - +
35A ALA* 3.8 22.6 - - + +
36A SER* 2.9 23.9 + - - -
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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) + - + + + + + -
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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