Contacts of the helix formed by residues 11 - 30 (chain A) in PDB entry 4Z2C
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 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A VAL 3.7 1.0 + - - -
10A ASN* 1.3 72.0 - - - +
12A THR* 1.3 59.2 + - - +
14A GLU* 3.4 2.2 + - + +
15A MET* 2.9 50.9 + - + +
519D LEU* 3.9 29.6 - - + +
523D TYR* 3.5 37.5 - - + -
530D LEU* 5.7 6.5 - - + -
610D VAL* 5.2 11.9 - - + -
611D SER 3.1 15.5 + - - +
612D VAL* 4.8 14.3 - - + +
613D ASP 5.7 0.2 - - - +
618D ALA* 5.0 6.1 - - + -
622D PHE* 3.6 19.5 - - + -
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Residues in contact with THR 12 (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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10A ASN* 3.4 2.8 - - - +
11A LEU* 1.3 78.8 - - - +
13A LYS* 1.3 56.7 + - - +
15A MET* 3.6 6.4 - - - +
16A LYS* 2.9 32.6 + - - +
617D GLU* 4.8 13.5 - - - -
618D ALA* 5.0 8.8 - - - +
621D ILE* 4.4 22.1 - - - +
622D PHE* 6.0 1.3 - - - -
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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
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10A ASN* 3.2 26.0 + - + +
11A LEU 3.2 0.6 - - - -
12A THR* 1.3 79.6 - - - +
14A GLU* 1.3 58.5 + - - +
16A LYS* 3.7 4.3 - - - +
17A ALA* 2.9 30.0 + - - +
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Residues in contact with GLU 14 (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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9A VAL* 4.8 10.8 - - + -
10A ASN 3.1 11.4 + - - +
11A LEU* 4.1 3.8 - - + +
13A LYS* 1.3 79.2 - - - +
15A MET* 1.3 57.3 + - - +
17A ALA* 4.3 6.3 - - + -
18A SER* 2.9 46.3 + - - +
515D ARG* 6.3 2.0 - - + -
519D LEU* 4.7 9.2 - - + -
537D ILE* 3.8 29.8 - - + -
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Residues in contact with MET 15 (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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11A LEU* 2.9 36.8 + - + +
12A THR* 3.6 7.6 - - - +
14A GLU* 1.3 77.6 - - - +
16A LYS* 1.3 57.1 + - - +
18A SER 3.9 0.2 - - - -
19A PHE* 2.9 33.8 + - - +
516D THR* 3.8 37.7 - - + +
519D LEU* 3.7 30.3 - - + -
621D ILE* 5.6 3.4 - - + -
622D PHE* 3.9 27.4 - - + -
625D LEU* 3.9 19.9 - - + +
626D MET* 4.2 18.8 - - + -
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Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR 2.9 19.2 + - - +
13A LYS* 3.7 4.9 - - - +
15A MET* 1.3 75.3 - - - +
17A ALA* 1.3 58.1 + - - +
19A PHE* 4.0 0.3 - - - +
20A ILE* 2.9 32.6 + - - +
621D ILE* 6.3 1.1 - - + -
625D LEU* 4.0 12.7 - - + +
636D PHE* 4.1 23.1 - - + -
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Residues in contact with ALA 17 (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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13A LYS 2.9 19.0 + - - +
14A GLU* 3.7 7.2 - - + +
16A LYS* 1.3 75.7 - - - +
18A SER* 1.3 64.0 + - - +
20A ILE* 3.2 6.7 + - - +
21A ASP* 2.9 27.1 + - - +
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Residues in contact with SER 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 GLU* 2.9 31.0 + - - +
17A ALA* 1.3 73.1 - - - +
19A PHE* 1.3 57.3 + - - +
21A ASP* 3.1 9.8 - - - +
22A TYR* 2.9 30.5 + - - +
512D ALA* 3.7 24.8 + - - +
515D ARG* 4.8 5.5 - - - +
516D THR* 3.6 20.4 - - - -
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Residues in contact with PHE 19 (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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15A MET* 2.9 19.4 + - + +
16A LYS 4.0 2.2 - - - +
18A SER* 1.3 75.1 - - - +
20A ILE* 1.3 61.7 + - - +
22A TYR* 4.9 9.9 - + - -
23A ALA* 2.9 43.2 + - + +
174A VAL* 3.7 17.9 - - + -
513D HIS* 5.4 8.5 - + - -
516D THR* 3.9 12.5 - - + +
625D LEU* 3.7 40.6 - - + -
626D MET* 4.2 20.4 - - - -
633D ARG* 3.4 40.8 - - + -
636D PHE* 4.4 10.5 - + - -
637D ILE* 6.3 2.0 - - + -
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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 LYS 2.9 19.8 + - - +
17A ALA* 3.6 5.2 - - - +
19A PHE* 1.3 79.1 - - - +
21A ASP* 1.3 57.1 + - - +
23A ALA* 3.7 4.7 - - - +
24A MET* 2.9 44.1 + - + +
636D PHE* 4.9 11.0 - - + -
640D ASN* 4.7 14.8 - - + +
641D ALA* 6.0 1.3 - - + -
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Residues in contact with ASP 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 ALA 2.9 14.2 + - - +
18A SER* 3.1 14.8 - - - +
20A ILE* 1.3 78.0 - - - +
22A TYR* 1.3 65.0 + - - +
24A MET* 3.9 3.3 - - - +
25A SER* 2.9 23.9 + - - -
509D VAL* 3.4 23.9 - - + +
512D ALA* 4.7 7.0 - - + +
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Residues in contact with TYR 22 (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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18A SER 2.9 14.1 + - - +
19A PHE* 4.2 10.1 - + - +
21A ASP* 1.3 77.1 - - - +
23A ALA* 1.3 64.3 + - + +
25A SER* 3.3 1.9 + - - -
26A VAL* 2.9 50.6 + - + +
30A ARG* 3.7 7.8 + - - -
174A VAL* 3.9 19.0 - - + +
458D LYS* 4.1 6.9 - - - +
509D VAL* 3.5 33.4 - - + +
510D ASP* 3.4 21.1 - - - -
513D HIS* 3.3 59.7 + + + +
14E A 6.1 0.2 + - - -
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Residues in contact with ALA 23 (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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19A PHE* 2.9 28.3 + - + +
20A ILE* 3.7 5.8 - - - +
22A TYR* 1.3 77.0 - - - +
24A MET* 1.3 66.1 + - + +
26A VAL* 3.0 4.3 + - - +
27A ILE* 2.9 37.0 + - + +
174A VAL* 4.1 30.5 - - + +
637D ILE* 5.6 7.0 - - + -
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Residues in contact with MET 24 (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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20A ILE* 2.9 29.5 + - - +
21A ASP* 3.9 2.7 - - - +
23A ALA* 1.3 73.9 - - + +
25A SER* 1.3 58.8 + - - +
27A ILE* 4.1 8.1 - - + -
28A VAL* 2.9 36.0 + - + +
641D ALA* 3.6 36.3 - - + -
642D VAL 4.3 16.6 - - - +
643D TYR* 4.5 20.0 - - + +
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Residues in contact with SER 25 (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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21A ASP 2.9 17.7 + - - -
22A TYR 3.5 5.2 - - - -
24A MET* 1.3 77.8 - - - +
26A VAL* 1.3 57.2 + - - +
29A ALA* 3.1 36.9 + - - +
30A ARG* 4.2 2.5 - - - +
509D VAL* 3.6 34.5 - - - -
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Residues in contact with VAL 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 TYR* 2.9 57.8 + - + +
23A ALA 3.0 3.6 + - - +
25A SER* 1.3 74.8 - - - +
27A ILE* 1.3 64.9 + - - +
30A ARG* 3.3 30.9 + - - +
31A ALA* 2.9 47.8 + - + +
172A ILE 4.7 1.1 - - - +
173A ALA* 3.9 15.7 - - - -
174A VAL* 4.0 11.7 - - + +
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Residues in contact with ILE 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 ALA* 2.9 33.4 + - + +
24A MET* 3.8 7.9 - - + +
26A VAL* 1.3 80.7 - - - +
28A VAL* 1.3 61.9 + - + +
29A ALA 3.6 0.2 + - - -
32A LEU* 3.6 35.5 + - + +
173A ALA* 4.5 2.9 - - + -
174A VAL 3.8 22.9 - - - +
176A MET* 3.6 35.7 - - + -
334A ILE* 3.6 6.1 - - + +
339A PRO* 3.9 21.3 - - + -
637D ILE* 4.9 9.0 - - + -
643D TYR* 4.0 17.9 - - + +
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Residues in contact with VAL 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 MET* 2.9 16.6 + - + +
27A ILE* 1.3 79.6 - - + +
29A ALA* 1.3 63.1 + - + +
30A ARG 4.0 0.2 - - - -
32A LEU 5.0 5.3 - - - +
41A PRO* 5.1 2.3 - - - +
334A ILE* 4.6 16.3 - - + +
337A GLY* 4.9 12.6 - - - +
339A PRO* 6.4 0.4 - - + -
643D TYR* 4.9 11.9 - - + -
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Residues in contact with ALA 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 SER* 3.1 18.2 + - - +
28A VAL* 1.3 82.6 - - + +
30A ARG* 1.3 65.2 + - - +
41A PRO* 3.6 26.7 - - + +
45A ARG* 6.3 0.7 - - - +
78A HIS* 5.8 3.5 - - - -
14E A 4.9 2.3 + - - -
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Residues in contact with ARG 30 (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 TYR* 3.7 8.7 + - - -
25A SER* 4.2 1.8 - - - +
26A VAL* 3.3 41.7 + - - +
28A VAL 4.0 0.2 - - - -
29A ALA* 1.3 80.9 + - - +
31A ALA* 1.3 66.3 + - + +
32A LEU 3.7 2.5 + - - +
40A LYS* 3.6 21.0 - - - +
41A PRO* 4.1 10.6 - - - +
42A VAL* 5.6 0.5 - - - +
78A HIS* 4.0 13.9 + - - -
458D LYS* 5.5 0.2 - - - +
509D VAL* 4.8 8.4 - - - +
510D ASP* 2.7 42.4 + - - -
13E T 3.9 26.9 + - - +
14E A 3.5 58.2 + - - +
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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
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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