Contacts of the helix formed by residues 15 - 32 (chain A) in PDB entry 2Z98
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 SER 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A SER* 3.2 24.7 - - - -
11A LEU* 3.5 4.8 + - - -
12A ALA 3.0 19.7 + - - -
13A GLY 3.2 0.6 - - - +
14A TYR* 1.3 78.2 - - - +
16A GLN* 1.2 60.8 + - - +
18A ASN* 2.9 24.4 + - - +
19A GLN* 3.1 27.7 + - - +
201A FMN 2.7 25.8 + - - -
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Residues in contact with GLN 16 (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 TYR 4.5 9.4 + - - +
15A SER* 1.2 71.0 - - - +
17A SER* 1.3 61.6 + - - +
19A GLN* 3.4 15.5 + - - +
20A LEU* 3.1 34.0 + - + +
139A SER* 4.3 8.5 - - - -
173A ALA* 5.6 0.7 - - + -
176A ILE* 3.8 31.0 - - + +
183A ALA* 5.8 1.2 - - - +
187A GLN* 3.0 39.1 + - - +
201A FMN 2.8 33.8 + - - +
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Residues in contact with SER 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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9A SER* 4.0 3.6 - - - -
15A SER* 3.5 1.7 + - - -
16A GLN* 1.3 74.3 - - - +
18A ASN* 1.3 59.2 + - - -
20A LEU* 3.5 7.5 + - - +
21A SER* 2.8 34.1 + - - -
92A ALA* 3.9 17.5 - - - +
94A PRO* 3.6 19.1 - - - +
137A ILE* 4.2 15.6 - - - +
139A SER* 3.4 15.5 - - - -
201A FMN 2.6 23.6 + - - -
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Residues in contact with ASN 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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7A LYS* 3.2 46.3 - - - +
8A SER 4.4 0.5 + - - -
9A SER* 4.1 13.7 + - - -
12A ALA* 3.4 26.7 + - - +
13A GLY* 5.8 1.3 - - - -
15A SER* 2.9 24.3 + - - +
17A SER* 1.3 75.0 + - - +
19A GLN* 1.3 62.7 + - + +
21A SER* 3.2 5.1 + - - -
22A ASP* 2.8 35.9 + - - +
41A ASP* 4.6 7.7 + - - -
92A ALA* 4.7 0.9 - - - +
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Residues in contact with GLN 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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13A GLY 3.6 20.2 - - - +
14A TYR* 3.9 11.6 - - - +
15A SER 3.1 23.7 + - - +
16A GLN* 3.7 18.4 + - - +
17A SER 3.3 0.2 - - - -
18A ASN* 1.3 76.7 - - + +
20A LEU* 1.3 58.3 + - + +
22A ASP* 3.4 9.6 + - - +
23A TYR* 3.1 26.0 + - - +
187A GLN* 5.3 6.7 - - - +
191A LYS* 5.3 12.7 + - - +
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Residues in contact with LEU 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 GLN* 3.1 25.3 + - + +
17A SER* 3.9 1.1 - - - +
19A GLN* 1.3 71.9 - - + +
21A SER* 1.3 65.9 + - - +
23A TYR* 3.2 5.5 + - - +
24A PHE* 2.9 22.9 + - - +
137A ILE* 3.9 28.0 - - + -
139A SER* 5.7 0.4 - - - -
173A ALA* 3.8 20.9 - - + -
186A ALA 5.4 0.4 - - - +
187A GLN* 4.3 11.2 - - + +
190A ALA* 3.8 30.5 - - + -
191A LYS* 3.8 39.0 - - + +
194A ILE* 3.8 13.8 - - + +
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Residues in contact with SER 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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5A VAL* 4.0 23.5 - - - +
7A LYS* 4.2 9.9 - - - -
17A SER 2.8 22.9 + - - -
18A ASN* 3.6 8.1 - - - -
20A LEU* 1.3 74.2 - - - +
22A ASP* 1.3 58.8 + - - +
24A PHE* 3.3 4.1 + - - +
25A VAL* 2.9 32.7 + - - +
90A VAL* 4.8 1.1 - - - +
92A ALA* 3.6 20.4 + - - +
137A ILE* 4.0 16.8 - - - +
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Residues in contact with ASP 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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7A LYS* 2.8 30.1 + - - -
18A ASN* 2.8 22.8 + - - +
19A GLN* 3.6 8.8 - - - +
20A LEU 3.3 0.2 - - - -
21A SER* 1.3 74.2 - - - +
23A TYR* 1.3 56.0 + - - +
25A VAL* 3.3 9.1 + - - +
26A GLU* 3.0 29.2 + - - +
39A VAL* 5.8 0.7 - - - +
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Residues in contact with TYR 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 GLN 3.1 13.2 + - - +
20A LEU* 3.2 11.6 + - - +
22A ASP* 1.3 72.4 - - - +
24A PHE* 1.3 66.3 + - - +
26A GLU* 3.2 19.4 + - - +
27A GLN* 3.0 52.1 + - + +
191A LYS* 3.8 56.6 - - + +
194A ILE* 3.9 17.3 - - + -
195A ASP* 2.5 35.4 + - - -
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Residues in contact with PHE 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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3A VAL* 4.3 9.6 - - + -
5A VAL* 5.1 0.4 - - + -
20A LEU 2.9 12.7 + - - +
21A SER* 3.4 12.8 - - - +
23A TYR* 1.3 72.7 - - - +
25A VAL* 1.3 75.3 + - + +
27A GLN* 3.3 2.0 + - - +
28A TRP* 2.8 62.1 + + + +
88A VAL* 4.7 0.7 - - + -
90A VAL* 3.6 34.8 - - + -
135A ILE* 4.3 18.4 - - + -
137A ILE* 4.4 9.9 - - + -
194A ILE* 3.6 31.9 - - + -
197A ILE* 4.2 16.2 - - + -
198A VAL* 4.1 10.3 - - + +
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Residues in contact with VAL 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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5A VAL* 3.7 30.1 - - + -
7A LYS* 6.5 0.2 - - - -
21A SER 2.9 22.7 + - - +
22A ASP* 3.3 10.0 + - - +
24A PHE* 1.3 80.0 - - + +
26A GLU* 1.3 64.5 + - - +
28A TRP* 3.4 4.4 + - - +
29A ARG* 2.9 38.4 + - + +
37A ILE* 4.1 26.5 - - + -
39A VAL* 4.4 13.0 - - + -
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Residues in contact with GLU 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 ASP 3.0 17.2 + - - +
23A TYR* 3.6 21.0 - - - +
25A VAL* 1.3 78.7 - - - +
27A GLN* 1.3 86.7 + - - +
29A ARG* 3.3 5.9 + - - +
30A GLU* 3.2 28.8 + - - +
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Residues in contact with GLN 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 TYR* 3.0 53.6 + - + +
24A PHE* 3.9 3.1 - - - +
26A GLU* 1.3 101.4 + - - +
28A TRP* 1.3 65.7 + - - +
30A GLU* 3.2 19.5 + - - +
31A LYS* 3.1 40.0 + - - +
195A ASP* 4.2 7.3 - - - +
198A VAL* 3.8 22.0 - - + -
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Residues in contact with TRP 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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1A SER* 5.5 2.7 - - - -
3A VAL* 3.4 28.9 - - + +
24A PHE* 2.8 49.7 + + + +
25A VAL 3.9 3.6 - - - +
27A GLN* 1.3 77.1 - - - +
29A ARG* 1.3 56.5 + - - +
32A HIS* 2.8 59.8 + + + +
35A ASP* 2.8 33.6 + - + -
37A ILE* 4.0 16.2 - - + -
88A VAL* 4.4 21.3 - - + -
135A ILE* 5.9 0.2 - - + -
197A ILE* 4.6 9.2 - - + -
198A VAL* 3.9 27.2 - - + +
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Residues in contact with ARG 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 VAL* 2.9 29.5 + - + +
26A GLU* 3.8 6.5 - - - +
27A GLN 3.3 0.2 - - - -
28A TRP* 1.3 75.7 - - - +
30A GLU* 1.3 60.5 + - - +
32A HIS 4.6 3.4 - - - -
33A SER* 2.5 61.3 + - - +
35A ASP 4.5 7.6 + - - -
37A ILE* 3.4 24.6 - - + +
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Residues in contact with GLU 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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26A GLU* 3.2 17.3 + - + +
27A GLN* 3.2 28.7 + - - +
28A TRP 3.1 1.0 - - - -
29A ARG* 1.3 79.1 - - - +
31A LYS* 1.3 65.2 + - + +
32A HIS 3.8 0.2 + - - -
33A SER* 5.0 2.3 + - - -
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Residues in contact with LYS 31 (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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27A GLN* 3.1 24.8 + - - +
30A GLU* 1.3 91.7 - - + +
32A HIS* 1.4 84.8 + - + +
33A SER 4.1 0.9 - - - -
198A VAL* 3.4 28.1 + - + -
199A SER* 3.5 38.4 - - - +
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Residues in contact with HIS 32 (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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28A TRP* 2.8 64.0 + + - +
29A ARG* 4.6 1.7 + - - -
31A LYS* 1.4 109.6 + - + +
33A SER* 1.4 53.7 + - - +
34A ALA* 3.3 4.5 - - - -
35A ASP* 3.1 33.4 + - - +
37A ILE* 6.0 0.2 - - - +
198A VAL* 2.8 30.2 + - + +
199A SER* 5.6 0.2 - - - -
200A ALA 5.3 4.7 + - - -
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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