Contacts of the helix formed by residues 30 - 41 (chain A) in PDB entry 5PN5
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 ASP 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLU 4.8 0.6 + - - -
27A GLU 4.2 6.8 + - - +
28A PHE 5.0 0.7 - - - -
29A ASN* 1.3 79.0 - - + +
31A PHE* 1.3 64.5 + - - +
32A ASP* 3.4 8.3 + - - +
33A LYS* 3.1 45.2 + - + +
34A TYR* 3.1 22.2 + - - +
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Residues in contact with PHE 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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29A ASN 3.6 5.0 + - - +
30A ASP* 1.3 72.7 + - - +
32A ASP* 1.3 78.1 + - - +
34A TYR* 3.1 4.3 + - - +
35A ILE* 3.0 49.7 + - + +
152A TRP* 3.5 48.4 - + + +
154A LEU* 5.3 0.2 - - + -
157A LEU* 4.1 32.3 - - + -
201A ILE* 3.6 31.4 - - + -
295A PHE* 4.1 26.9 - + + -
405A EDO 4.2 19.2 + - - -
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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
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30A ASP* 3.4 7.4 + - - +
31A PHE* 1.3 94.0 - - - +
33A LYS* 1.3 63.6 + - - +
35A ILE* 3.3 6.1 + - - +
36A ALA* 3.0 22.7 + - - +
158A GLY 6.0 0.3 + - - -
166A LYS* 4.8 11.3 + - - -
295A PHE* 5.9 1.2 - - - -
296A ALA 5.3 4.9 - - - +
297A THR* 5.6 7.8 - - + +
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Residues in contact with LYS 33 (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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30A ASP* 3.1 37.1 + - + +
32A ASP* 1.3 76.6 - - - +
34A TYR* 1.3 59.7 + - - +
36A ALA* 3.4 6.5 + - - +
37A TYR* 2.9 27.7 + - + +
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Residues in contact with TYR 34 (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 PHE* 3.4 30.6 - - + +
22A HIS 4.1 1.9 + - - -
23A PRO* 3.6 37.4 - - + +
27A GLU* 3.8 39.1 + - + +
30A ASP 3.1 14.3 + - - +
31A PHE 3.1 6.0 + - - +
33A LYS* 1.3 75.8 - - - +
35A ILE* 1.3 65.3 + - - +
37A TYR* 3.2 30.5 + + + +
38A MET* 2.9 55.2 + - + +
51A ILE* 4.4 2.7 - - + -
152A TRP* 3.9 21.8 - + + -
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Residues in contact with ILE 35 (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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31A PHE* 3.0 50.4 + - + +
32A ASP* 3.7 7.6 - - - +
34A TYR* 1.3 75.8 - - - +
36A ALA* 1.4 63.9 + - - +
38A MET* 3.2 20.7 + - + +
39A GLU* 3.0 30.6 + - + +
152A TRP* 4.4 6.5 - - + -
199A TYR* 4.1 26.0 - - + -
273A VAL* 4.3 16.4 - - + -
275A PHE* 4.8 4.5 - - + -
295A PHE* 4.2 12.1 - - + -
297A THR* 4.2 15.5 - - + -
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Residues in contact with ALA 36 (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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32A ASP 3.0 16.3 + - - +
33A LYS* 3.7 7.6 - - - +
35A ILE* 1.4 78.8 - - - +
37A TYR* 1.3 61.5 + - - +
39A GLU* 3.3 11.3 + - - +
40A SER* 2.9 22.3 + - - -
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Residues in contact with TYR 37 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A PHE* 4.2 15.2 - + - -
27A GLU* 6.2 1.3 - - - -
33A LYS* 2.9 17.0 + - + +
34A TYR* 3.2 39.9 + + + +
36A ALA* 1.3 77.2 - - - +
38A MET* 1.3 65.9 + - + +
40A SER* 2.6 28.5 + - - -
41A GLN* 3.2 44.7 + - + +
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Residues in contact with MET 38 (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 PHE* 3.8 28.5 - - + -
34A TYR* 2.9 54.2 + - + +
35A ILE* 3.2 21.7 + - + +
37A TYR* 1.3 72.4 - - - +
39A GLU* 1.3 61.5 + - - +
41A GLN* 3.1 11.1 + - - +
42A GLY 3.3 0.3 + - - -
43A ALA* 3.0 26.2 + - + +
49A ALA* 3.6 31.0 - - + -
51A ILE* 3.8 26.2 - - + -
152A TRP* 4.8 0.2 - - - -
273A VAL* 4.8 3.4 - - + -
275A PHE* 4.2 13.7 - - + -
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Residues in contact with GLU 39 (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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35A ILE* 3.0 19.3 + - - +
36A ALA* 3.7 11.9 - - - +
38A MET* 1.3 72.8 - - - +
40A SER* 1.3 61.9 + - - +
42A GLY* 2.9 15.9 + - - -
43A ALA 4.3 0.4 - - - +
44A HIS* 3.2 33.8 - - + +
199A TYR* 2.6 34.7 + - - -
275A PHE* 3.4 15.2 - - + -
297A THR* 5.0 0.9 + - - -
299A ARG* 3.0 39.6 + - - +
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Residues in contact with SER 40 (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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12A GLN* 3.5 19.2 - - - +
36A ALA 2.9 13.9 + - - -
37A TYR* 2.6 28.5 + - - -
39A GLU* 1.3 75.8 - - - +
41A GLN* 1.3 74.7 + - - +
42A GLY 3.3 0.7 - - - -
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Residues in contact with GLN 41 (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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12A GLN* 3.5 31.7 + - - +
13A ASN* 4.0 4.0 + - - +
19A MET* 3.5 29.6 - - + +
21A PHE* 4.5 4.9 - - + -
37A TYR* 3.5 47.2 + - + +
38A MET 3.1 8.5 + - - +
39A GLU 3.0 1.0 - - - -
40A SER* 1.3 98.3 + - - +
42A GLY* 1.3 59.4 + - - +
43A ALA 3.4 1.1 - - - -
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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