Contacts of the helix formed by residues 20 - 34 (chain B) in PDB entry 2P2M
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 ASN 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B CYS* 3.8 14.2 - - - -
19B ILE* 1.3 74.4 - - - +
21B PRO* 1.4 70.6 - - + +
22B GLU* 3.0 14.2 + - - +
23B GLN* 2.8 51.5 + - - +
24B TYR 2.9 24.3 + - - -
428B GLY 3.6 4.5 - - - -
429B ALA* 3.5 6.3 - - - +
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Residues in contact with PRO 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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9B ILE* 4.4 8.7 - - + -
20B ASN* 1.4 90.4 - - + +
22B GLU* 1.3 61.2 + - - +
24B TYR* 3.5 3.7 + - + +
25B GLU* 3.2 28.3 + - - +
428B GLY 3.4 12.1 - - - +
429B ALA* 3.6 27.8 - - + +
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Residues in contact with GLU 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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20B ASN* 3.0 10.9 + - - +
21B PRO* 1.3 76.6 - - - +
23B GLN* 1.3 62.2 - - + +
25B GLU* 3.3 7.4 + - + +
26B THR* 3.0 41.9 + - - +
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Residues in contact with GLN 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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17B CYS 5.0 1.4 - - - +
18B LEU 3.3 17.6 + - - +
19B ILE* 3.9 11.9 - - + -
20B ASN* 2.8 49.3 + - - +
22B GLU* 1.3 76.3 - - + +
24B TYR* 1.3 59.0 + - - +
26B THR* 3.9 5.2 - - - -
27B LYS* 2.9 43.5 + - + +
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Residues in contact with TYR 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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19B ILE* 3.4 9.3 - - + +
20B ASN 2.9 13.5 + - - +
21B PRO* 3.7 7.4 - - + +
22B GLU 3.3 0.2 - - - -
23B GLN* 1.3 76.1 - - - +
25B GLU* 1.3 78.4 + - + +
28B TYR* 2.9 49.4 + + + +
426B LEU* 4.6 13.5 - - + -
429B ALA* 3.8 17.3 - - + -
430B ILE* 4.4 18.2 - - + -
439B ARG* 3.3 38.2 - - + +
440B PRO* 2.7 32.7 + - - +
442B PHE* 3.5 30.0 - + - -
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Residues in contact with GLU 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 PRO* 3.2 15.3 + - + +
22B GLU* 3.3 9.6 + - + +
24B TYR* 1.3 99.6 - - + +
26B THR* 1.3 62.9 + - - +
28B TYR* 4.1 5.7 - - - +
29B LYS* 3.2 24.8 + - - +
439B ARG* 4.4 14.0 + - - -
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Residues in contact with THR 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 GLU* 3.0 25.8 + - - +
23B GLN* 3.9 6.1 - - - -
25B GLU* 1.3 74.9 - - - +
27B LYS* 1.3 67.5 + - + +
29B LYS* 3.5 5.4 + - - +
30B GLN* 3.1 23.1 + - + +
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Residues in contact with LYS 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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19B ILE* 3.7 24.9 - - + -
23B GLN* 2.9 27.3 + - - +
26B THR* 1.3 76.3 - - + +
28B TYR* 1.3 61.2 + - - +
30B GLN* 3.4 3.7 + - - +
31B SER* 2.9 29.8 + - - -
38B PHE* 3.7 26.5 - - + -
42B GLN* 5.4 6.3 - - - +
291B TYR* 4.9 10.8 + - + -
442B PHE* 3.5 33.7 - - + -
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Residues in contact with TYR 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 TYR* 2.9 34.0 + + + +
25B GLU* 4.1 6.1 - - - +
27B LYS* 1.3 76.2 - - - +
29B LYS* 1.3 67.4 + - - +
31B SER* 2.7 24.0 + - - -
32B ILE* 3.1 35.1 + - + +
440B PRO* 3.6 31.4 - - + +
441B PHE 3.4 22.9 - - - -
442B PHE* 3.7 8.2 - - + -
444B VAL 2.7 30.6 + - - -
445B GLN* 4.1 6.2 - - - +
446B PRO* 4.1 2.3 - - - +
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Residues in contact with LYS 29 (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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25B GLU 3.2 17.1 + - - +
26B THR* 3.7 6.1 - - - +
28B TYR* 1.3 83.9 - - - +
30B GLN* 1.3 57.4 + - - +
32B ILE* 3.2 4.8 + - - +
33B ASN* 2.8 46.1 + - - +
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Residues in contact with GLN 30 (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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26B THR* 3.1 19.3 + - + +
27B LYS* 3.9 5.9 - - - +
29B LYS* 1.3 76.0 - - - +
31B SER* 1.3 57.9 + - - +
33B ASN* 4.5 3.1 - - - +
34B ASP* 2.8 48.8 + - + +
37B THR* 3.6 25.7 - - - +
38B PHE* 3.6 29.9 - - + +
41B GLU* 4.2 11.0 + - - +
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Residues in contact with SER 31 (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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27B LYS 2.9 14.6 + - - -
28B TYR* 2.7 24.4 + - - -
30B GLN* 1.3 75.8 - - - +
32B ILE* 1.3 61.5 + - - +
35B PRO* 3.4 26.0 - - - +
38B PHE* 3.6 33.1 - - - +
39B TRP* 4.6 0.9 + - - -
442B PHE* 3.7 1.9 - - - -
443B GLY* 2.8 35.4 + - - -
445B GLN* 5.6 0.5 + - - -
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Residues in contact with ILE 32 (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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28B TYR* 3.1 44.9 + - + +
29B LYS* 3.8 3.6 - - - +
31B SER* 1.3 90.8 - - - +
33B ASN* 1.3 71.6 + - - +
35B PRO* 3.8 9.2 - - - +
443B GLY* 3.8 20.4 - - - +
445B GLN* 3.5 49.7 + - + +
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Residues in contact with ASN 33 (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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29B LYS* 2.8 35.9 + - - +
30B GLN* 4.5 2.7 - - - +
32B ILE* 1.3 83.2 - - - +
34B ASP* 1.3 61.6 + - + +
35B PRO* 3.6 4.4 - - - +
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Residues in contact with ASP 34 (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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30B GLN* 2.8 28.9 + - + +
33B ASN* 1.3 78.8 - - + +
35B PRO* 1.4 60.9 - - - +
36B ASP* 3.9 8.0 + - - +
37B THR* 2.7 35.4 + - - +
38B PHE 3.0 22.2 + - - -
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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