Contacts of the helix formed by residues 11 - 28 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL 3.5 1.0 + - - -
10B ASN* 1.3 74.0 - - - +
12B THR* 1.3 59.0 + - - +
13B LYS 3.2 0.3 + - - -
14B GLU* 3.3 2.3 + - + +
15B MET* 2.9 49.2 + - + +
519C LEU* 3.9 21.8 - - + +
523C TYR* 3.7 22.9 - - + -
530C LEU* 6.1 2.5 - - + -
610C VAL* 3.6 30.1 - - + -
611C SER 3.5 6.9 + - - -
612C VAL* 4.1 28.6 - - + +
613C ASP 5.4 0.6 - - - +
618C ALA* 5.0 3.1 - - + -
622C PHE* 3.6 31.0 - - + -
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Residues in contact with THR 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASN* 3.5 2.1 - - - +
11B LEU* 1.3 80.0 - - - +
13B LYS* 1.3 56.7 + - - +
15B MET* 3.7 7.0 - - - +
16B LYS* 2.9 31.4 + - - +
613C ASP* 6.5 1.3 - - - -
617C GLU* 5.3 7.0 - - - -
618C ALA* 5.2 12.0 - - - +
621C ILE* 4.9 17.0 - - - +
622C PHE* 6.1 1.8 - - - -
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Residues in contact with LYS 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASN* 3.4 26.4 + - + +
11B LEU 3.1 0.6 - - - -
12B THR* 1.3 78.8 - - - +
14B GLU* 1.3 58.1 + - - +
16B LYS* 3.2 6.1 + - - +
17B ALA* 2.9 30.6 + - - +
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 5.2 9.6 - - + -
10B ASN 3.2 12.3 + - - +
11B LEU* 4.0 3.4 - - + +
13B LYS* 1.3 76.5 - - - +
15B MET* 1.3 60.9 + - - +
17B ALA* 4.5 4.9 - - - -
18B SER* 2.9 46.8 + - - +
515C ARG* 4.1 24.7 - - - +
519C LEU* 4.7 7.2 - - + -
537C ILE* 4.3 17.3 - - + -
610C VAL* 6.5 0.2 - - + -
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Residues in contact with MET 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 2.9 36.8 + - + +
12B THR* 3.7 7.4 - - - +
14B GLU* 1.3 76.2 - - - +
16B LYS* 1.3 58.3 + - - +
18B SER* 4.1 2.8 - - - -
19B PHE* 2.9 34.0 + - - +
516C THR* 3.6 33.5 + - + +
519C LEU* 3.7 32.5 - - + +
520C THR* 4.2 4.0 - - + -
621C ILE* 5.6 4.7 - - + +
622C PHE* 3.7 34.1 - - + +
625C LEU* 4.1 18.1 - - + +
626C MET* 4.4 8.3 - - + -
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Residues in contact with LYS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR 2.9 20.0 + - - +
13B LYS* 3.5 5.4 - - - +
15B MET* 1.3 75.4 - - - +
17B ALA* 1.3 56.6 + - - +
19B PHE* 3.9 0.9 - - - +
20B ILE* 2.9 32.6 + - - +
625C LEU* 4.3 11.4 - - + +
636C PHE* 4.4 21.6 - - + -
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Residues in contact with ALA 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LYS 2.9 16.7 + - - +
14B GLU* 4.0 6.1 - - - +
16B LYS* 1.3 77.5 - - - +
18B SER* 1.3 63.0 + - - +
20B ILE* 3.4 5.4 + - - +
21B ASP* 2.9 24.9 + - - +
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Residues in contact with SER 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLU* 2.9 22.8 + - - +
15B MET* 4.1 1.1 - - - -
17B ALA* 1.3 75.2 - - - +
19B PHE* 1.3 58.8 + - - +
21B ASP* 3.2 6.8 + - - +
22B TYR* 2.9 29.8 + - - +
512C ALA* 3.9 23.3 - - - +
515C ARG* 3.6 29.3 + - - -
516C THR* 3.8 16.6 - - - -
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Residues in contact with PHE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B MET 2.9 20.3 + - - +
16B LYS 3.9 2.0 - - - +
18B SER* 1.3 74.7 - - - +
20B ILE* 1.3 62.2 + - - +
22B TYR* 3.3 12.6 + + + +
23B ALA* 2.9 41.4 + - + +
174B VAL* 3.9 16.2 - - + -
513C HIS* 5.5 7.2 - + - -
516C THR* 4.2 13.4 + - + +
625C LEU* 3.5 55.0 - - + -
626C MET* 4.5 12.6 - - + -
633C ARG* 3.5 36.3 - - + -
636C PHE* 4.5 9.9 - + - -
637C ILE* 5.7 3.4 - - + -
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Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LYS 2.9 18.9 + - - +
17B ALA* 3.8 4.7 - - - +
19B PHE* 1.3 78.9 - - - +
21B ASP* 1.3 57.5 + - - +
23B ALA* 3.9 5.0 - - - +
24B MET* 2.9 34.4 + - - +
636C PHE* 5.1 8.7 - - + -
640C ASN 4.5 15.9 - - - +
641C ALA* 5.5 5.8 - - + -
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Residues in contact with ASP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ALA 2.9 13.9 + - - +
18B SER* 3.3 12.6 - - - +
20B ILE* 1.3 77.2 - - - +
22B TYR* 1.3 63.4 + - - +
24B MET* 3.9 2.4 - - - +
25B SER* 3.0 27.4 + - - -
509C VAL* 4.4 10.3 - - + +
512C ALA* 4.9 7.2 - - + -
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Residues in contact with TYR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B SER 2.9 15.4 + - - +
19B PHE* 3.9 9.9 - + + +
21B ASP* 1.3 75.5 - - - +
23B ALA* 1.3 59.6 + - + +
25B SER* 3.3 1.4 + - - -
26B VAL* 2.9 44.8 + - + +
30B ARG* 3.5 27.5 + - - -
174B VAL* 3.8 26.3 - - + +
509C VAL* 3.4 37.2 + - + +
510C ASP* 3.9 7.4 + - - -
513C HIS* 3.3 58.8 + + + +
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 2.9 28.7 + - + +
20B ILE* 3.9 4.9 - - - +
22B TYR* 1.3 76.8 - - + +
24B MET* 1.3 57.6 + - - +
26B VAL* 3.1 3.3 + - - +
27B ILE* 2.9 40.7 + - + +
174B VAL* 3.8 33.4 - - + -
637C ILE* 5.0 10.5 - - + -
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Residues in contact with MET 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ILE 2.9 19.3 + - - +
21B ASP* 3.9 3.1 - - - +
23B ALA* 1.3 76.4 - - - +
25B SER* 1.3 58.5 + - - +
27B ILE* 3.8 9.0 - - - +
28B VAL* 2.9 35.4 + - + +
641C ALA* 5.2 10.5 - - + -
643C TYR* 4.9 17.5 - - + -
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Residues in contact with SER 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ASP 3.0 18.6 + - - -
22B TYR 3.7 3.1 - - - -
24B MET* 1.3 77.9 - - - +
26B VAL* 1.3 61.0 + - - +
29B ALA* 3.3 34.4 + - - +
30B ARG* 4.1 2.2 - - - +
509C VAL* 3.7 32.8 - - - -
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TYR* 2.9 43.9 + - + +
23B ALA 3.7 3.4 - - - +
25B SER* 1.3 75.2 - - - +
27B ILE* 1.3 63.8 + - - +
30B ARG* 3.3 41.4 - - - +
31B ALA* 2.9 46.3 + - + +
172B ILE 5.3 0.4 - - - +
173B ALA* 4.2 8.7 - - - -
174B VAL* 4.0 19.5 - - + +
509C VAL* 5.8 0.2 - - + -
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Residues in contact with ILE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ALA* 2.9 30.1 + - + +
24B MET* 3.8 6.1 - - - +
26B VAL* 1.3 79.8 - - - +
28B VAL* 1.3 62.6 + - + +
29B ALA 3.3 2.9 + - - -
32B LEU* 3.5 49.6 + - + +
173B ALA* 4.6 7.4 - - + -
174B VAL 3.8 24.2 - - - +
176B MET* 3.8 20.4 - - + -
334B ILE* 3.6 7.6 - - + +
339B PRO* 3.8 23.3 - - + -
637C ILE* 5.1 8.1 - - + -
643C TYR* 4.4 14.4 - - + +
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B MET 2.9 14.9 + - - +
25B SER 4.3 0.2 - - - -
27B ILE* 1.3 78.8 - - + +
29B ALA* 1.3 63.2 + - + +
32B LEU 5.6 1.3 - - - -
41B PRO* 5.4 0.2 - - - +
334B ILE* 4.3 16.8 - - + +
337B GLY* 4.1 19.7 - - - +
643C TYR* 4.9 10.8 - - + -
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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
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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