Contacts of the helix formed by residues 29 - 39 (chain d) in PDB entry 4PJO
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 29 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1252 A 5.1 2.9 - - - +
23d GLU 5.4 0.4 + - - -
24d PHE* 3.5 42.2 - - + +
27d GLY 3.3 1.2 - - - -
28d PRO* 1.3 73.2 - - - +
30d SER* 1.3 63.5 + - - +
31d VAL 3.0 2.0 - - - +
32d LEU* 3.1 18.1 + - + +
33d THR* 3.0 13.0 + - - -
59d PHE* 3.8 10.6 - - + -
60d ASP 3.8 11.7 - - - +
61d ARG* 3.8 21.1 - - - +
63d CYS* 4.6 6.5 - - - -
37f ASP* 4.3 7.2 - - - +
41f ASN* 3.6 27.6 - - + +
63f LEU* 4.1 28.3 - - + -
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Residues in contact with SER 30 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24d PHE 3.2 20.5 + - - -
25d ASN* 3.6 17.3 - - - -
26d THR 4.1 2.3 + - - -
27d GLY 3.0 20.2 + - - -
28d PRO 3.0 0.8 + - - -
29d LEU* 1.3 76.7 - - - +
31d VAL* 1.3 56.8 + - - +
33d THR* 3.4 4.7 - - - -
34d GLN* 2.9 41.0 + - - +
43f GLN* 3.1 22.0 + - - -
61f GLU* 4.9 1.0 + - - -
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Residues in contact with VAL 31 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28d PRO 3.1 16.1 + - - +
29d LEU 3.0 0.2 - - - -
30d SER* 1.3 76.8 + - - +
32d LEU* 1.3 66.6 + - + +
35d SER* 2.7 35.2 + - - +
109d VAL* 4.7 5.2 - - + -
111d ARG* 3.5 30.5 - - + +
43f GLN* 3.9 19.5 - - + +
61f GLU* 3.9 24.9 - - + +
62f VAL 4.3 1.6 - - - -
63f LEU* 4.0 28.5 - - + +
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Residues in contact with LEU 32 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29d LEU* 3.1 10.4 + - + +
31d VAL* 1.3 86.7 - - + +
33d THR* 1.3 55.2 + - - +
34d GLN 3.1 1.8 - - - -
35d SER* 2.8 10.0 + - - +
36d VAL* 2.7 36.5 + - + +
42d VAL* 5.4 1.1 - - + -
56d VAL* 5.1 2.5 - - + -
59d PHE* 3.3 46.4 - - + -
63d CYS* 4.3 15.5 - - + -
65d MET* 4.3 24.7 - - + -
109d VAL* 4.1 17.7 - - + -
63f LEU* 3.9 31.6 - - + -
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Residues in contact with THR 33 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-3c GLY 4.1 2.4 - - - +
-2c SER* 3.6 29.2 - - - -
24d PHE* 2.9 32.3 + - + +
25d ASN* 4.0 22.4 - - - +
29d LEU 3.0 8.7 + - - -
30d SER* 3.2 5.2 + - - -
32d LEU* 1.3 76.1 - - - +
34d GLN* 1.3 62.6 + - - +
36d VAL* 3.7 4.7 + - - +
37d LYS* 3.0 33.7 + - - +
59d PHE* 3.4 15.5 - - + -
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Residues in contact with GLN 34 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25d ASN* 5.4 3.8 + - - +
30d SER* 2.9 25.1 + - - +
31d VAL* 4.8 0.4 - - - -
33d THR* 1.3 81.9 - - - +
35d SER* 1.3 58.7 + - - +
37d LYS* 3.3 26.3 + - - +
38d ASN* 2.9 50.1 + - - +
111d ARG* 2.9 27.4 + - - +
61f GLU* 5.6 3.1 - - - +
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Residues in contact with SER 35 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31d VAL 2.7 21.7 + - - -
32d LEU* 2.8 9.6 + - - -
34d GLN* 1.3 74.2 - - - +
36d VAL* 1.3 59.5 + - - -
39d ASN* 2.9 25.1 + - - -
40d THR* 3.0 28.6 + - - +
42d VAL* 3.9 7.2 - - - +
56d VAL* 4.2 20.7 + - - +
111d ARG* 3.0 26.9 - - - +
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Residues in contact with VAL 36 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-3c GLY* 3.7 26.5 - - - +
-2c SER* 4.0 5.8 - - - +
32d LEU 2.7 21.0 + - - +
33d THR* 3.7 5.4 - - - +
35d SER* 1.3 72.6 - - - +
37d LYS* 1.3 67.0 + - - +
39d ASN* 3.4 6.6 + - - -
56d VAL* 3.5 39.0 - - + +
57d LYS* 3.9 21.1 - - - +
58d ALA* 4.3 1.8 - - - +
59d PHE* 4.0 17.0 - - + -
58k THR 3.9 4.5 - - - +
59k ARG 3.8 15.4 - - - +
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Residues in contact with LYS 37 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-3c GLY* 3.1 27.1 - - - +
-2c SER* 5.7 1.3 - - - -
25d ASN* 4.4 13.9 + - - -
33d THR* 3.0 20.2 + - + +
34d GLN* 3.3 25.5 + - - +
36d VAL* 1.3 82.4 - - - +
38d ASN* 1.3 71.7 - - - +
39d ASN 3.6 0.2 + - - -
57k PRO* 3.5 15.9 - - - +
58k THR 4.0 0.2 - - - +
59k ARG* 3.3 51.9 - - + +
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Residues in contact with ASN 38 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34d GLN* 2.9 32.5 + - - +
37d LYS* 1.3 85.8 - - - +
39d ASN* 1.3 71.3 + - - +
40d THR* 3.2 20.3 + - + +
111d ARG* 4.2 11.5 - - - +
55k PRO 4.8 3.6 - - - +
57k PRO* 4.1 19.8 - - + +
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Residues in contact with ASN 39 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35d SER 2.9 9.9 + - - -
36d VAL* 3.4 5.2 + - - +
37d LYS 3.3 3.4 - - - -
38d ASN* 1.3 79.5 - - - +
40d THR* 1.3 60.8 + - - +
55d ARG* 2.8 48.8 + - - +
56d VAL 5.5 3.1 - - - +
57d LYS* 5.8 4.2 - - - +
49k GLU* 4.8 0.2 - - - +
54k ALA* 5.7 1.0 - - - +
55k PRO* 3.1 33.2 - - + +
56k PRO 3.6 10.2 + - - +
57k PRO* 4.0 15.5 - - + -
58k THR* 4.4 20.5 - - - +
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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