Contacts of the helix formed by residues 24 - 37 (chain B) in PDB entry 4DTZ
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 LYS 24 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B THR* 3.1 10.3 + - - +
23B ASP* 1.4 91.9 - - + +
25B PRO* 1.4 64.8 - - - +
27B GLN* 3.3 29.6 + - + +
28B ALA* 3.0 22.2 + - - +
432B ASP* 2.7 29.7 + - - +
433B ILE 3.4 20.9 + - - +
434B LYS* 5.2 2.0 - - - +
435B GLU* 3.3 16.2 - - + +
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Residues in contact with PRO 25 (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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20B LEU* 4.1 27.9 - - + +
22B THR* 3.4 24.4 - - + +
23B ASP 3.4 9.2 - - - +
24B LYS* 1.4 89.7 - - - +
26B VAL* 1.3 58.7 + - + +
28B ALA* 3.3 3.1 + - + +
29B LEU* 2.9 34.3 + - + +
185B MET* 6.2 4.5 - - + -
435B GLU* 3.2 16.8 - - + +
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PRO* 1.3 74.5 - - + +
27B GLN* 1.4 58.7 + - + +
29B LEU* 3.2 12.8 + - + +
30B MET* 2.9 38.4 + - - +
329B PRO* 3.7 41.1 - - + -
330B ALA* 5.3 6.7 - - + -
356B LEU* 4.3 13.9 - - + -
358B PRO* 4.2 16.2 - - + -
435B GLU* 2.8 25.0 + - - +
439B LEU* 4.7 6.5 - - + -
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Residues in contact with GLN 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LYS* 3.6 24.5 + - + +
25B PRO 3.3 0.2 - - - -
26B VAL* 1.4 76.1 - - + +
28B ALA* 1.3 64.3 + - - +
30B MET* 3.3 10.5 + - - +
31B LYS* 3.1 30.2 + - - +
325B TRP* 4.5 22.0 - - + -
433B ILE* 2.9 55.6 + - + +
435B GLU* 2.8 30.0 + - - +
439B LEU* 5.8 0.9 - - + -
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Residues in contact with ALA 28 (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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19B LEU* 4.4 8.3 - - + +
20B LEU* 6.2 0.7 - - + -
22B THR* 4.4 11.9 - - + +
24B LYS 3.0 13.7 + - - +
25B PRO* 3.6 11.0 - - + +
26B VAL 3.2 0.2 - - - -
27B GLN* 1.3 79.3 - - - +
29B LEU* 1.3 62.8 + - + +
31B LYS* 3.2 9.6 + - - +
32B ILE* 3.0 30.7 + - + +
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 4.0 23.1 - - + -
25B PRO* 2.9 26.4 + - + +
26B VAL* 3.2 13.7 + - + +
28B ALA* 1.3 70.6 - - + +
30B MET* 1.3 60.9 + - - +
32B ILE* 3.3 15.2 + - + +
33B ALA* 2.9 28.6 + - - +
40B PHE* 3.9 25.0 - - + -
42B PHE* 4.3 5.2 - - + -
51B TYR* 3.5 42.0 - - + +
356B LEU* 3.7 19.7 - - + +
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Residues in contact with MET 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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26B VAL* 2.9 27.0 + - + +
27B GLN* 3.5 12.3 - - - +
28B ALA 3.2 0.2 - - - -
29B LEU* 1.3 76.5 - - - +
31B LYS* 1.3 61.0 + - + +
33B ALA* 3.3 2.8 + - - +
34B ASP* 2.9 33.3 + - - +
325B TRP* 3.7 33.4 - - + -
356B LEU* 4.0 9.2 - - + -
358B PRO* 3.6 32.8 - - + -
359B GLN* 3.4 32.0 + - + +
362B ARG* 3.9 16.8 - - - +
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Residues in contact with LYS 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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27B GLN* 3.1 17.4 + - - +
28B ALA* 3.5 9.2 - - - +
30B MET* 1.3 78.1 - - + +
32B ILE* 1.3 63.3 + - + +
34B ASP* 3.3 20.5 + - + +
35B GLU* 3.2 22.8 + - - +
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Residues in contact with ILE 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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8B PRO* 3.8 15.9 - - + -
19B LEU* 3.9 35.2 - - + -
28B ALA* 3.0 23.9 + - + +
29B LEU* 3.6 25.4 - - + +
30B MET 3.2 0.2 - - - -
31B LYS* 1.3 77.0 - - + +
33B ALA* 1.3 51.5 - - - +
35B GLU* 3.1 10.7 + - + +
36B LEU* 2.8 56.1 + - + +
40B PHE* 3.7 17.9 - - + -
42B PHE* 5.4 0.2 - - + -
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Residues in contact with ALA 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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29B LEU 2.9 17.4 + - - +
30B MET 3.6 5.2 - - - +
32B ILE* 1.3 73.1 - - - +
34B ASP* 1.3 61.6 + - - +
37B GLY* 2.8 38.0 + - - +
40B PHE* 3.8 15.2 - - + -
53B SER* 3.4 26.5 - - - +
356B LEU* 4.1 1.3 - - + -
359B GLN* 3.7 17.5 - - + +
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Residues in contact with ASP 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 MET* 2.9 19.0 + - - +
31B LYS* 3.4 28.8 + - + +
32B ILE 3.2 0.4 - - - -
33B ALA* 1.3 77.8 - - - +
35B GLU* 1.3 61.1 + - - +
37B GLY* 4.5 1.6 + - - -
359B GLN* 3.1 20.7 + - - +
362B ARG* 5.9 0.9 - - - -
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Residues in contact with GLU 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 LYS 3.2 10.0 + - - +
32B ILE* 3.1 12.8 + - - +
34B ASP* 1.3 81.9 - - - +
36B LEU* 1.3 74.6 + - + +
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Residues in contact with LEU 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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6B PRO* 3.8 33.0 - - + +
7B GLN 3.7 34.5 - - - +
8B PRO* 3.7 8.1 - - + -
32B ILE* 2.8 35.9 + - + +
35B GLU* 1.3 92.5 - - + +
37B GLY* 1.3 59.3 + - - +
38B GLU 4.3 0.2 + - - -
39B ILE 4.4 1.5 - - - +
40B PHE* 3.7 21.5 - - + -
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Residues in contact with GLY 37 (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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33B ALA* 2.8 39.3 + - - +
34B ASP 4.5 1.7 + - - -
35B GLU 3.7 1.2 - - - -
36B LEU* 1.3 73.1 - - - +
38B GLU* 1.3 64.7 + - - -
39B ILE* 3.1 7.2 + - - -
40B PHE* 4.5 2.9 - - - -
53B SER* 4.3 3.9 + - - -
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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