Contacts of the helix formed by residues 35 - 44 (chain C) in PDB entry 3P05
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 GLU 35 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C LYS* 2.9 52.9 - - - +
33C SER* 2.6 31.8 + - - -
34C PRO* 1.3 71.5 - - - +
36C VAL* 1.3 65.5 + - - +
37C ILE 3.0 1.4 + - - -
38C PRO* 3.4 9.1 - - - +
39C MET* 3.2 20.8 + - - +
173C ARG* 3.8 13.8 - - - +
232C IOD 3.4 9.7 - - - +
57D ASN 3.5 19.2 - - - +
58D THR* 3.7 6.4 - - - +
59D VAL 4.0 5.2 - - - +
60D GLY* 3.6 15.1 - - - -
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Residues in contact with VAL 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TRP* 4.4 22.8 - - + -
26C VAL* 4.6 9.6 - - + +
27C VAL* 4.5 7.0 - - + -
30C LYS* 4.0 23.8 - - + -
31C ALA 3.4 21.8 - - - +
32C PHE* 4.3 18.8 - - + -
33C SER 3.0 17.9 + - - +
35C GLU* 1.3 78.6 - - - +
37C ILE* 1.3 61.0 + - + +
39C MET* 3.6 6.8 - - - +
40C PHE* 2.8 27.4 + - + +
138C LEU* 5.1 7.4 - - + -
142C VAL* 5.6 0.9 - - + -
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Residues in contact with ILE 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C PRO* 3.1 9.1 + - + +
35C GLU 3.0 1.4 - - - -
36C VAL* 1.3 77.4 - - + +
38C PRO* 1.3 72.2 - - + +
40C PHE* 3.2 8.0 + - - +
41C SER* 2.9 27.8 + - - +
135C ILE* 4.3 27.4 - - + +
138C LEU* 4.0 19.3 - - + -
139C ASN* 3.0 47.1 - - - +
142C VAL* 4.1 16.2 - - + -
176C GLN* 4.6 3.6 - - + +
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Residues in contact with PRO 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C PRO 3.5 7.6 - - - +
35C GLU 3.4 11.4 - - - +
37C ILE* 1.3 98.1 - - + +
39C MET* 1.3 56.1 + - - +
41C SER* 3.2 8.4 + - - -
42C ALA* 2.8 31.5 + - - +
173C ARG* 3.8 10.1 - - - +
54D THR* 4.9 4.7 - - + +
57D ASN* 3.6 38.4 - - + +
58D THR* 4.1 7.2 - - + -
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Residues in contact with MET 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C CYS* 4.9 4.7 - - - -
23C TRP* 5.2 2.0 - - + -
26C VAL* 4.0 29.8 - - + -
30C LYS* 3.6 21.5 - - - +
35C GLU 3.2 15.7 + - - +
36C VAL* 3.6 7.0 - - - +
37C ILE 3.1 0.2 - - - -
38C PRO* 1.3 80.3 - - - +
40C PHE* 1.3 57.5 + - - +
42C ALA* 3.3 2.1 + - - +
43C LEU* 2.9 46.7 + - + +
20D LEU* 4.0 21.1 - - - +
24D VAL* 3.6 15.7 - - + -
58D THR* 3.3 36.3 - - - +
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Residues in contact with PHE 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TRP* 3.8 35.5 - + + -
36C VAL 2.8 21.1 + - - +
37C ILE 3.5 4.3 - - - +
39C MET* 1.3 72.5 - - - +
41C SER* 1.3 65.3 + - - +
43C LEU* 3.3 3.5 + - - +
44C SER* 2.9 29.0 + - - -
52C LEU* 3.8 26.7 - - + -
55C MET* 3.9 21.5 - - + -
56C LEU* 4.8 9.6 - - + -
131C LYS* 3.9 21.3 - - + -
134C ILE* 3.5 32.3 - - + -
135C ILE* 4.0 16.2 - - + -
138C LEU* 4.0 20.6 - - + -
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Residues in contact with SER 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ILE* 2.9 17.3 + - - +
38C PRO* 3.5 11.1 - - - +
40C PHE* 1.3 74.6 - - - +
42C ALA* 1.3 63.5 + - - +
44C SER* 3.1 19.1 + - - -
45C GLU* 3.5 19.1 + - - +
131C LYS* 3.5 9.7 + - - +
135C ILE* 3.6 24.6 - - - +
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Residues in contact with ALA 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C PRO 2.8 19.1 + - - +
39C MET 3.8 1.6 - - - +
41C SER* 1.3 74.2 - - - +
43C LEU* 1.3 65.1 + - - +
44C SER 3.4 0.5 + - - -
45C GLU* 4.0 19.3 + - - +
15D ILE* 4.6 16.9 - - + +
17D PRO* 6.0 1.0 - - - +
20D LEU* 3.5 29.8 - - + -
54D THR* 3.6 19.1 - - + +
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C THR* 3.7 24.1 - - + +
22C CYS* 4.3 15.0 - - + -
23C TRP* 3.7 46.9 - - + +
39C MET* 2.9 35.0 + - + +
40C PHE 3.9 3.4 - - - +
41C SER 3.2 0.2 - - - -
42C ALA* 1.3 79.2 - - - +
44C SER* 1.3 59.2 + - - +
45C GLU 3.6 1.3 + - - +
55C MET* 4.1 14.5 - - + +
17D PRO* 4.2 34.4 - - + +
20D LEU* 4.7 10.8 - - + -
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Residues in contact with SER 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C PHE* 2.9 23.8 + - - -
41C SER* 3.1 2.1 + - - -
43C LEU* 1.3 79.8 - - - +
45C GLU* 1.3 65.0 + - - +
46C GLY 3.2 1.0 + - - -
47C ALA* 3.1 20.2 + - - +
52C LEU* 3.9 23.3 - - - -
55C MET* 4.0 12.8 - - - -
131C LYS* 3.0 37.5 + - - +
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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