Contacts of the helix formed by residues 31 - 41 (chain D) in PDB entry 1CCW
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 ASP 31 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D LYS 5.9 0.4 - - - +
29D GLU 3.5 6.5 + - - +
30D VAL* 1.3 72.7 - - - +
32D LEU* 1.3 59.3 + - - +
33D GLN* 3.2 19.8 + - - +
34D GLU* 3.0 27.7 + - + +
35D ALA* 2.8 31.0 + - - +
164D ALA* 5.3 0.6 - - - +
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Residues in contact with LEU 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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17D ARG* 3.4 49.8 - - - +
30D VAL* 4.0 4.3 + - + +
31D ASP* 1.3 71.7 + - - +
33D GLN* 1.3 64.4 + - - +
35D ALA* 3.7 3.3 - - + +
36D VAL* 3.1 30.0 + - - +
160D GLU* 4.5 2.2 - - - +
200D LEU* 4.3 9.2 - - + -
203D PHE* 3.3 44.2 - - + -
204D TYR* 3.4 32.1 - - + +
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Residues in contact with GLN 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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31D ASP* 3.2 9.6 + - - +
32D LEU* 1.3 81.7 - - - +
34D GLU* 1.3 63.7 + - - +
36D VAL* 3.5 11.3 + - - +
37D ASP* 3.6 17.7 + - - +
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Residues in contact with GLU 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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29D GLU 5.4 2.6 - - - +
31D ASP* 3.0 31.1 + - + +
33D GLN* 1.3 80.0 - - - +
35D ALA* 1.3 58.6 + - - +
37D ASP* 3.3 8.2 + - - +
38D TYR* 3.0 26.9 + - - +
136D ARG* 2.8 43.3 + - - -
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Residues in contact with ALA 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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31D ASP 2.8 16.7 + - - +
32D LEU* 3.7 6.1 - - + +
33D GLN 3.3 0.2 - - - -
34D GLU* 1.3 79.8 + - - +
36D VAL* 1.3 59.7 + - - +
38D TYR* 3.3 1.4 + - - +
39D LEU* 2.8 36.9 + - + +
136D ARG* 3.9 7.6 - - - +
164D ALA* 3.9 26.2 - - + -
204D TYR* 3.6 22.2 - - - +
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Residues in contact with VAL 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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32D LEU 3.1 17.0 + - - +
33D GLN* 3.9 6.5 - - - +
34D GLU 3.4 0.2 - - - -
35D ALA* 1.3 74.7 - - - +
37D ASP* 1.3 70.1 + - - +
39D LEU* 3.4 1.6 + - - +
40D LYS* 3.0 35.2 + - + +
203D PHE* 4.2 7.4 - - + -
204D TYR* 3.9 24.5 - - + -
207D GLN* 4.1 29.2 - - + -
209D VAL* 4.0 18.6 - - + -
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Residues in contact with ASP 37 (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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33D GLN* 3.6 13.6 + - - +
34D GLU* 3.3 9.4 + - + +
35D ALA 3.3 0.6 - - - -
36D VAL* 1.3 86.5 - - - +
38D TYR* 1.3 62.6 + - - +
40D LYS* 3.3 10.5 + - - +
41D LYS* 3.2 30.8 + - + +
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Residues in contact with TYR 38 (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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34D GLU* 3.0 12.5 + - - +
35D ALA 3.3 7.2 + - - +
37D ASP* 1.3 76.5 - - - +
39D LEU* 1.3 65.7 + - + +
41D LYS* 3.1 17.8 + - + +
42D ILE* 3.5 11.9 + - + +
136D ARG* 3.5 62.3 - - + +
139D LEU* 3.6 17.3 - - + +
140D GLU* 2.6 41.2 + - + +
164D ALA 4.1 5.4 - - - -
166D GLY* 4.0 22.2 - - - -
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Residues in contact with LEU 39 (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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35D ALA* 2.8 22.0 + - + +
36D VAL 3.7 4.0 - - - +
38D TYR* 1.3 74.3 - - + +
40D LYS* 1.3 62.3 + - - +
42D ILE* 3.0 32.0 + - + +
47D ASN* 5.5 4.3 + - - -
163D HIS 3.5 27.6 - - - +
164D ALA 5.4 0.2 - - - +
166D GLY* 3.8 19.5 - - - -
167D TRP 4.9 0.7 - - - +
168D THR* 3.9 17.9 - - + -
204D TYR* 3.4 40.6 - - + +
209D VAL* 3.8 22.1 - - + +
211D ILE* 4.6 6.5 - - + -
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Residues in contact with LYS 40 (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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36D VAL* 3.0 29.6 + - + +
37D ASP* 3.8 10.8 - - - +
38D TYR 3.3 0.4 - - - -
39D LEU* 1.3 75.7 - - - +
41D LYS* 1.3 61.1 + - + +
42D ILE 3.6 5.4 + - - +
207D GLN 2.8 29.1 + - - -
208D GLY* 4.0 12.5 - - - +
209D VAL* 3.7 19.3 - - + -
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Residues in contact with LYS 41 (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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37D ASP* 3.2 16.9 + - + +
38D TYR* 3.1 13.9 + - + +
40D LYS* 1.3 76.4 - - - +
42D ILE* 1.3 63.6 + - - +
43D PRO* 3.4 6.8 - - - +
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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