Contacts of the helix formed by residues 29 - 36 (chain C) in PDB entry 4KEU
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 29 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A PRO* 3.8 12.7 - - - +
104A PHE* 4.0 7.5 + - - +
105A TYR* 3.4 24.6 + - - +
28C PHE* 1.3 74.6 - - - +
30C GLU* 1.3 68.9 + - - +
31C ALA* 4.5 1.3 - - - -
32C VAL* 3.2 21.8 + - - +
33C ARG* 3.0 19.4 + - - +
40C TYR* 4.3 0.2 + - - -
71C GLY 4.7 5.3 + - - -
262C ASP* 2.8 15.3 + - - -
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Residues in contact with GLU 30 (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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30A GLU* 4.3 0.9 - - - -
31A ALA* 3.6 32.5 - - + +
34A GLN* 3.4 36.6 - - + +
35A GLN* 3.0 23.4 + - - +
28C PHE* 3.5 7.0 + - - -
29C SER* 1.3 70.4 - - - +
31C ALA* 1.3 57.8 + - - +
33C ARG* 3.5 1.0 + - - +
34C GLN* 3.0 32.7 + - - +
70C MET* 3.6 1.7 - - - -
71C GLY* 2.9 44.1 + - - -
73C GLY* 3.1 15.7 + - - -
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Residues in contact with ALA 31 (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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30A GLU* 3.7 28.5 - - + +
31A ALA* 5.6 0.9 - - + +
70A MET* 3.8 29.6 - - + -
71A GLY* 4.6 1.6 - - - +
103A PRO* 5.0 6.3 - - + -
29C SER* 3.2 1.4 - - - -
30C GLU* 1.3 79.0 - - - +
32C VAL* 1.3 59.4 + - - +
34C GLN* 3.8 0.5 - - - +
35C GLN* 3.0 35.2 + - - +
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Residues in contact with VAL 32 (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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70A MET* 4.3 3.6 - - - -
103A PRO* 4.0 9.6 - - + -
105A TYR* 3.9 19.3 - - + -
106A PHE* 3.7 28.3 - - + -
29C SER* 3.2 22.1 + - - +
31C ALA* 1.3 75.4 - - - +
33C ARG* 1.3 59.9 + - - +
36C TRP* 2.8 43.7 + - + +
39C LEU* 3.9 23.1 - - + -
40C TYR* 3.5 18.8 - - - +
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Residues in contact with ARG 33 (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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26C ARG* 3.3 13.4 - - - +
28C PHE* 3.5 55.8 - - + +
29C SER 3.0 6.5 + - - +
30C GLU 4.1 0.7 - - - +
32C VAL* 1.3 76.7 - - - +
34C GLN* 1.3 62.6 + - - +
37C PRO* 3.3 25.6 - - + +
40C TYR* 3.3 51.5 + - + +
42C GLU* 4.0 16.8 + - - +
45C GLU* 2.8 43.4 + - - -
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Residues in contact with GLN 34 (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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28A PHE* 3.4 34.6 - - - -
30A GLU* 3.4 30.7 - - + +
33A ARG* 6.0 0.2 - - - +
34A GLN* 3.8 16.9 + - - +
74A ARG 4.3 8.5 + - - -
75A ASP* 5.6 2.2 + - - +
127A GLN* 3.0 25.3 - - - +
30C GLU 3.0 16.1 + - - +
31C ALA 3.8 3.8 - - - +
33C ARG* 1.3 80.3 - - - +
35C GLN* 1.3 64.9 + - - +
37C PRO* 3.7 4.0 - - - +
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Residues in contact with GLN 35 (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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30A GLU* 2.8 27.8 + - - +
70A MET* 3.5 23.5 - - + +
74A ARG* 2.8 77.7 + - - +
127A GLN* 3.1 22.2 + - - +
31C ALA 3.0 18.1 + - - +
34C GLN* 1.3 80.7 - - - +
36C TRP* 1.3 86.1 + - + +
37C PRO* 3.5 2.2 - - - +
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Residues in contact with TRP 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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70A MET* 3.7 32.1 - - + -
74A ARG* 4.3 5.4 - - - -
94A THR* 4.0 12.1 - - - -
95A GLY 3.6 24.2 - - - -
96A ILE* 3.7 17.0 - - + -
106A PHE* 4.5 4.3 - + - -
117A LEU* 3.4 43.7 + - + -
118A PHE* 4.2 4.3 - + - -
120A HIS* 4.7 0.4 - + - -
121A ASP* 3.0 32.5 + - - -
32C VAL* 2.8 25.6 + - + +
33C ARG 3.7 2.7 - - - -
35C GLN* 1.3 95.7 - - + +
37C PRO* 1.3 66.1 - - - +
38C HIS* 3.0 34.0 + + + -
39C LEU* 3.1 26.1 + - + +
40C TYR* 3.8 3.6 - - - -
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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