Contacts of the helix formed by residues 32 - 43 (chain D) in PDB entry 3C5C
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 GLY 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D GLY 3.3 0.4 - - - -
31D ALA* 1.3 80.2 - - - +
33D LYS* 1.3 66.0 + - - +
34D SER 3.4 2.2 - - - -
35D ALA* 3.9 0.2 - - - +
36D LEU* 3.1 33.5 + - - +
97D VAL* 4.6 0.9 - - - -
134D ASN* 3.5 9.5 + - - -
201D GDP 3.0 34.0 + - - -
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Residues in contact with LYS 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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25D ILE* 3.7 29.4 - - + +
26D LEU* 3.3 37.5 - - - +
27D GLY* 3.1 12.7 + - - +
28D ARG 3.1 21.4 + - - +
29D ARG* 3.7 3.4 - - - +
31D ALA* 5.0 0.2 - - + -
32D GLY* 1.3 77.4 - - - +
34D SER* 1.3 61.4 + - - +
36D LEU* 3.5 3.0 + - - +
37D THR* 2.8 27.7 + - - -
74D ASP* 3.4 11.4 - - - +
75D THR* 3.1 26.5 - - - -
76D ALA* 4.7 4.9 - - - +
77D ASP 5.2 1.1 + - - +
97D VAL* 4.2 11.0 - - + +
201D GDP 2.6 37.5 + - - +
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Residues in contact with SER 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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33D LYS* 1.3 73.6 - - - +
35D ALA* 1.3 61.1 + - - +
37D THR* 3.3 1.5 + - - -
38D VAL* 2.8 37.3 + - - +
49D TYR* 3.3 33.4 - - - -
53D LEU 4.6 0.7 + - - -
74D ASP* 2.5 25.7 + - - -
201D GDP 2.9 11.1 + - - -
202D MG 2.2 30.2 - - - -
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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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32D GLY 3.9 1.8 - - - +
33D LYS 3.4 0.4 - - - -
34D SER* 1.3 71.7 - - - +
36D LEU* 1.3 57.3 + - - +
38D VAL* 3.7 3.8 - - - +
39D LYS* 2.8 32.1 + - - +
44D ARG 4.9 0.9 - - - +
45D PHE* 3.8 14.5 - - + -
46D ILE 4.4 12.3 - - - +
165D ALA* 3.5 16.7 - - + +
201D GDP 2.8 47.0 + - + +
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Residues in contact with LEU 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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25D ILE* 6.0 1.8 - - + -
32D GLY 3.1 21.3 + - - +
33D LYS 4.0 3.1 - - - +
35D ALA* 1.3 74.4 - - - +
37D THR* 1.3 60.5 + - - +
39D LYS* 4.2 1.6 - - - -
40D PHE* 2.9 28.9 + - - +
95D LEU* 6.3 0.2 - - + -
97D VAL* 3.9 21.1 - - + -
132D LEU* 4.2 15.0 - - + -
134D ASN* 3.3 33.7 - - - +
163D VAL* 3.9 21.1 - - + -
164D SER 4.0 2.5 - - - -
165D ALA* 3.7 20.4 - - + +
172D VAL* 3.6 17.9 - - + +
175D VAL* 6.1 0.9 - - + -
176D PHE* 3.6 17.7 - - + -
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Residues in contact with THR 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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25D ILE* 4.0 15.9 - - - +
33D LYS 2.8 23.4 + - - -
34D SER* 3.3 6.7 + - - -
36D LEU* 1.3 76.9 - - - +
38D VAL* 1.3 53.2 + - + +
40D PHE* 3.2 3.3 + - + +
41D LEU* 2.8 59.4 + - + +
57D TYR* 4.3 14.4 - - + -
72D VAL* 3.8 25.5 - - + +
74D ASP* 4.0 13.0 - - + +
176D PHE* 4.1 9.1 - - + -
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Residues in contact with VAL 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 SER* 2.8 25.1 + - - +
35D ALA* 4.0 4.5 - - - +
37D THR* 1.3 71.7 - - - +
39D LYS* 1.3 55.1 + - - +
41D LEU* 4.3 11.2 - - + -
42D THR* 2.7 55.8 + - + -
44D ARG 3.7 5.8 - - - +
46D ILE* 3.3 36.1 - - + +
49D TYR* 3.9 36.1 - - + +
57D TYR* 5.3 4.7 - - + -
74D ASP* 5.8 0.2 - - - +
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Residues in contact with LYS 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 19.9 + - - +
36D LEU* 3.8 7.2 - - - +
38D VAL* 1.3 74.4 - - - +
40D PHE* 1.3 59.8 + - - +
43D LYS* 3.0 52.4 + - - -
44D ARG* 3.4 10.6 + - - +
45D PHE* 4.1 8.5 - - - +
165D ALA* 2.8 32.8 + - + +
166D CYS* 3.7 6.5 - - - +
167D LEU 2.9 28.6 + - - -
168D ASP 4.1 0.7 - - - -
169D PHE* 3.4 24.2 - - - +
172D VAL* 4.1 23.6 - - + -
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Residues in contact with PHE 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 LEU 2.9 17.2 + - - +
37D THR* 3.5 4.0 - - - +
39D LYS* 1.3 76.3 - - - +
41D LEU* 1.3 72.6 + - + +
43D LYS* 5.1 0.5 + - - +
59D SER* 4.0 4.7 - - - -
61D GLU* 3.4 38.7 - - + +
70D LEU* 3.2 31.9 - - + -
72D VAL* 4.6 4.9 - - + -
169D PHE* 3.3 25.1 - + - -
172D VAL* 4.1 5.3 - - + +
173D GLN* 3.9 20.9 - - + -
176D PHE* 3.5 47.8 - + + -
177D HIS* 4.0 14.6 - + - -
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Residues in contact with LEU 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 THR* 2.8 39.5 + - + +
38D VAL* 4.1 7.9 - - + +
40D PHE* 1.3 86.9 - - + +
42D THR* 1.3 66.9 + - + +
43D LYS* 5.2 5.2 + - - +
57D TYR* 3.3 52.9 - - + +
58D SER 4.5 5.6 - - - +
59D SER* 4.3 25.4 - - - +
72D VAL* 5.1 3.4 - - + -
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Residues in contact with THR 42 (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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38D VAL* 2.7 41.5 + - + +
41D LEU* 1.3 82.5 - - + +
43D LYS* 1.3 68.9 + - - +
44D ARG* 2.8 30.7 + - - +
46D ILE* 5.2 1.9 - - + +
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Residues in contact with LYS 43 (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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65A HIS* 5.5 10.5 + - - -
39D LYS* 3.0 33.6 + - - +
40D PHE 5.1 0.6 + - - +
41D LEU 3.7 5.2 + - - +
42D THR* 1.3 78.6 - - - +
44D ARG* 1.3 55.7 + - - +
169D PHE* 3.7 48.7 - - + +
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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