Contacts of the helix formed by residues 29 - 36 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 1.4 73.3 - - - +
30A GLU* 1.3 69.3 + - - +
31A ALA 3.2 1.3 - - - -
32A VAL* 3.2 25.2 + - - +
33A ARG* 3.1 19.1 + - - +
40A TYR* 4.3 0.2 + - - -
71A GLY 4.7 0.9 - - - -
262A ASP* 3.0 7.4 + - - -
103C PRO* 3.7 12.6 - - - +
104C PHE* 3.3 18.8 - - - -
105C TYR* 3.2 28.8 + - - +
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Residues in contact with GLU 30 (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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28A PHE* 3.4 9.1 + - - -
29A SER* 1.3 70.8 - - - +
31A ALA* 1.3 58.0 + - - +
33A ARG* 4.0 1.4 - - - +
34A GLN* 3.0 31.6 + - - +
70A MET* 3.5 1.7 - - - -
71A GLY* 2.9 43.2 + - - +
73A GLY* 3.2 14.4 + - - -
30C GLU* 4.3 1.3 - - - -
31C ALA* 3.7 30.5 - - + +
34C GLN* 3.4 34.8 - - - +
35C GLN* 2.8 25.3 + - - +
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Residues in contact with ALA 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 SER* 3.2 1.6 - - - -
30A GLU* 1.3 75.9 - - - +
32A VAL* 1.3 59.1 + - - +
34A GLN* 3.5 0.5 + - - +
35A GLN* 2.9 35.9 + - - +
30C GLU* 3.6 30.2 - - + +
31C ALA* 5.6 0.9 - - + +
70C MET* 3.8 30.3 - - + -
71C GLY* 4.6 1.6 - - - +
103C PRO* 5.0 7.0 - - + -
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Residues in contact with VAL 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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29A SER* 3.2 25.2 + - - +
31A ALA* 1.3 74.9 - - - +
33A ARG* 1.3 56.9 + - - +
35A GLN 3.1 0.7 + - - -
36A TRP* 2.7 46.8 + - + +
39A LEU* 3.9 24.0 - - + -
40A TYR* 3.3 19.1 - - - +
70C MET* 4.4 2.9 - - - -
103C PRO* 4.0 8.1 - - + -
105C TYR* 3.8 17.7 - - + -
106C PHE* 3.7 28.9 - - + -
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Residues in contact with ARG 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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26A ARG* 3.4 16.7 - - - +
28A PHE* 3.6 52.7 - - + +
29A SER 3.1 4.3 + - - +
30A GLU 4.0 0.4 - - - +
32A VAL* 1.3 80.4 - - - +
34A GLN* 1.3 62.8 + - - +
37A PRO* 3.4 24.6 - - + +
40A TYR* 3.4 46.4 - - + +
42A GLU* 4.1 16.8 + - - +
45A GLU* 2.7 45.9 + - - -
34C GLN* 6.0 0.2 - - - +
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Residues in contact with GLN 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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30A GLU 3.0 16.5 + - - +
31A ALA 3.8 3.4 - - - +
33A ARG* 1.3 80.2 - - - +
35A GLN* 1.3 63.1 + - - +
37A PRO* 4.0 3.5 - - - +
28C PHE* 3.5 32.8 - - - -
30C GLU* 3.4 33.5 - - + +
33C ARG* 5.7 0.4 - - - +
34C GLN* 3.8 16.2 - - - +
74C ARG 4.4 8.1 + - - -
75C ASP* 5.3 4.4 + - - +
127C GLN* 2.8 25.9 - - - +
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Residues in contact with GLN 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 ALA 2.9 21.6 + - - +
34A GLN* 1.3 81.8 - - - +
36A TRP* 1.3 82.3 + - + +
37A PRO* 3.5 6.2 - - - +
30C GLU* 3.0 25.9 + - - +
70C MET* 3.5 23.6 - - + +
73C GLY 3.9 0.8 - - - -
74C ARG* 2.8 85.0 + - - +
127C GLN* 3.1 17.6 + - - +
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Residues in contact with TRP 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 VAL* 2.7 31.0 + - + +
33A ARG 3.8 0.4 - - - -
35A GLN* 1.3 89.4 - - + +
37A PRO* 1.4 65.1 - - - +
38A HIS* 3.1 26.8 + + + -
39A LEU* 3.2 31.7 + - + +
40A TYR* 3.8 2.6 - - - -
70C MET* 3.6 35.4 - - + -
74C ARG* 4.2 4.9 - - - -
94C THR* 4.1 6.5 - - - -
95C GLY 3.6 24.7 - - - -
96C ILE* 3.7 14.6 - - + -
106C PHE* 4.5 3.8 - + - -
117C LEU* 3.4 45.3 + - + -
118C PHE* 4.2 4.0 - + - -
120C HIS* 4.8 0.7 - + - -
121C ASP* 3.0 37.1 + - - -
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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