Contacts of the helix formed by residues 29 - 36 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B PRO* 3.7 13.2 - - - +
104B PHE* 3.8 10.4 + - - +
105B TYR* 3.4 25.1 + - - +
28D PHE* 1.3 73.9 - - - +
30D GLU* 1.3 69.7 + - - +
31D ALA 3.3 1.3 - - - -
32D VAL* 3.2 25.1 + - - +
33D ARG* 3.0 18.9 + - - +
40D TYR* 4.2 0.2 + - - -
71D GLY 4.7 4.3 - - - -
262D ASP* 3.0 12.7 + - - -
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Residues in contact with GLU 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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30B GLU* 4.4 1.1 - - - -
31B ALA* 3.7 32.7 - - + +
34B GLN* 3.4 32.5 - - + +
35B GLN* 3.2 18.2 + - - +
28D PHE* 3.5 7.3 + - - -
29D SER* 1.3 71.4 - - - +
31D ALA* 1.3 58.3 + - - +
33D ARG* 3.5 1.6 + - - +
34D GLN* 3.0 33.2 + - - +
70D MET* 3.5 1.4 - - - -
71D GLY* 2.7 45.8 + - - -
73D GLY* 3.1 23.3 + - - -
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Residues in contact with ALA 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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30B GLU* 3.7 36.0 - - + +
31B ALA* 5.5 1.3 - - + +
70B MET* 3.9 24.5 - - + -
71B GLY* 5.1 0.7 - - - -
103B PRO* 5.0 6.1 - - + -
29D SER* 3.3 1.4 - - - -
30D GLU* 1.3 78.4 - - - +
32D VAL* 1.3 57.4 + - - +
34D GLN* 3.8 0.7 - - - +
35D GLN* 3.0 35.0 + - - +
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Residues in contact with VAL 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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70B MET* 4.3 4.3 - - - -
103B PRO* 3.8 12.3 - - + -
105B TYR* 3.8 22.4 - - + -
106B PHE* 3.7 26.9 - - + -
29D SER* 3.2 23.8 + - - +
31D ALA* 1.3 74.7 - - - +
33D ARG* 1.3 58.5 + - - +
35D GLN 3.8 0.5 - - - -
36D TRP* 2.8 43.4 + - + +
39D LEU* 3.9 18.8 - - + -
40D TYR* 3.6 17.5 - - - +
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Residues in contact with ARG 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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26D ARG* 3.4 15.1 - - - +
28D PHE* 3.4 49.0 - - + +
29D SER 3.0 16.9 + - - +
30D GLU 4.0 1.6 - - - +
32D VAL* 1.3 76.9 - - - +
34D GLN* 1.3 63.6 + - - +
37D PRO* 3.3 26.5 - - + +
40D TYR* 3.3 48.0 - - + +
42D GLU* 3.8 20.0 + - - +
45D GLU* 2.8 43.6 + - - -
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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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28B PHE* 3.7 25.5 - - - -
30B GLU* 3.5 42.4 - - + +
33B ARG* 6.0 0.2 - - - +
34B GLN* 3.8 15.1 - - - +
74B ARG 4.4 4.0 + - - -
75B ASP* 5.7 2.4 + - - +
127B GLN* 3.0 23.8 - - - +
30D GLU 3.0 16.0 + - - +
31D ALA 3.8 4.0 - - - +
33D ARG* 1.3 80.5 - - - +
35D GLN* 1.3 67.5 + - - +
37D PRO* 4.0 4.0 - - - +
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Residues in contact with GLN 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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30B GLU* 3.1 27.0 + - - +
70B MET* 3.5 23.8 - - + +
74B ARG* 2.8 76.6 + - - +
127B GLN* 3.1 22.9 + - - +
31D ALA 3.0 18.1 + - - +
34D GLN* 1.3 80.4 - - - +
36D TRP* 1.3 86.2 + - + +
37D PRO* 3.5 3.5 - - - +
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Residues in contact with TRP 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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70B MET* 3.6 35.7 - - + -
74B ARG* 4.2 5.8 - - - -
94B THR* 4.1 6.7 - - - -
95B GLY 3.6 24.9 - - - -
96B ILE* 3.7 13.9 - - + -
106B PHE* 4.6 4.3 - + - -
117B LEU* 3.4 47.4 + - + -
118B PHE* 4.2 4.0 - + - -
120B HIS* 4.8 0.7 - + - -
121B ASP* 2.9 34.8 + - - -
32D VAL* 2.8 22.0 + - + +
33D ARG 3.7 3.1 - - - -
35D GLN* 1.3 93.1 - - + +
37D PRO* 1.3 66.2 - - - +
38D HIS* 3.1 25.9 + + + -
39D LEU* 3.2 32.2 + - + +
40D TYR* 3.8 4.7 - - - -
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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