Contacts of the helix formed by residues 29 - 36 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B PHE* 1.3 74.4 - - - +
30B GLU* 1.3 68.5 + - - +
31B ALA 3.2 1.1 - - - -
32B VAL* 3.1 24.9 + - - +
33B ARG 3.0 18.7 + - - -
40B TYR* 4.2 0.3 + - - -
71B GLY 4.9 5.1 + - - -
262B ASP* 2.9 10.6 + - - -
103D PRO* 3.7 13.9 - - - +
104D PHE* 3.8 7.8 + - - +
105D TYR* 3.3 27.9 + - - +
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B PHE* 3.4 8.1 + - - -
29B SER* 1.3 70.4 - - - +
31B ALA* 1.3 63.4 + - - +
33B ARG* 3.4 1.7 + - - +
34B GLN* 3.1 25.6 + - - +
70B MET* 3.6 1.6 - - - -
71B GLY* 2.8 41.5 + - - +
73B GLY* 3.0 20.9 + - - -
30D GLU* 4.5 1.3 - - - -
31D ALA* 3.7 33.2 - - + +
34D GLN* 3.5 37.1 - - - +
35D GLN* 3.1 17.9 + - - +
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B SER* 3.2 1.0 - - - -
30B GLU* 1.3 78.5 - - - +
32B VAL* 1.3 63.7 + - - +
34B GLN* 3.5 0.9 + - - +
35B GLN* 3.0 30.5 + - - +
30D GLU* 3.7 30.2 - - + +
31D ALA* 5.0 1.5 - - + +
70D MET* 3.8 29.2 - - + -
71D GLY* 4.6 0.9 - - - +
103D PRO* 5.0 7.4 - - + -
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Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B SER* 3.1 25.0 + - - +
31B ALA* 1.3 77.5 - - - +
33B ARG* 1.3 56.8 + - - +
35B GLN 3.2 0.5 + - - -
36B TRP* 2.9 43.6 + - + +
39B LEU* 4.1 13.5 - - + -
40B TYR* 3.3 23.8 - - + +
70D MET* 4.4 3.6 - - - -
103D PRO* 4.0 10.3 - - + -
105D TYR* 3.8 21.8 - - + -
106D PHE* 3.7 28.7 - - + -
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Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ARG* 3.2 15.0 - - - +
28B PHE* 3.5 55.1 - - + +
29B SER 3.0 6.2 + - - +
30B GLU 4.0 1.1 - - - +
32B VAL* 1.3 77.4 - - - +
34B GLN* 1.3 62.4 + - - +
37B PRO* 3.4 25.3 - - + +
40B TYR* 3.2 50.9 - - + +
42B GLU* 3.9 17.6 - - - +
45B GLU* 2.7 44.5 + - - -
34D GLN* 6.0 0.2 - - - +
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Residues in contact with GLN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLU 3.1 16.0 + - - +
31B ALA 3.9 3.8 - - - +
33B ARG* 1.3 80.9 - - - +
35B GLN* 1.3 61.5 + - - +
36B TRP 3.9 0.2 + - - -
37B PRO* 4.0 3.8 - - - +
28D PHE* 3.5 31.4 - - - -
30D GLU* 3.4 32.3 - - + +
34D GLN* 3.8 16.7 - - - +
74D ARG 4.4 9.3 + - - -
75D ASP* 5.4 4.2 + - - +
127D GLN* 2.9 27.0 - - - +
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Residues in contact with GLN 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ALA 3.0 20.3 + - - +
34B GLN* 1.3 80.2 - - - +
36B TRP* 1.3 85.5 + - + +
37B PRO* 3.5 3.1 - - - +
30D GLU* 3.2 23.9 + - - +
70D MET* 3.5 24.2 - - + +
73D GLY 3.9 1.2 - - - -
74D ARG* 2.7 86.0 + - - +
121D ASP* 4.4 0.2 - - - +
127D GLN* 3.3 21.8 + - - +
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Residues in contact with TRP 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B VAL* 2.9 26.2 + - + +
33B ARG 3.7 3.1 - - - -
35B GLN* 1.3 96.7 + - + +
37B PRO* 1.3 63.2 - - - +
38B HIS* 3.1 36.2 + + + -
39B LEU* 3.2 23.9 + - + +
40B TYR* 3.7 5.9 - - - -
70D MET* 3.6 45.3 - - + -
74D ARG* 4.3 2.5 - - - -
94D THR* 4.3 1.6 - - - -
95D GLY 4.0 9.6 - - - -
96D ILE* 3.8 17.9 - - + -
106D PHE* 4.4 4.9 - + - -
117D LEU* 3.4 44.7 + - + -
118D PHE* 4.3 7.9 - + - -
120D HIS* 4.7 0.2 - + - -
121D ASP* 2.9 35.6 + - - -
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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