Contacts of the helix formed by residues 45 - 58 (chain D) in PDB entry 1Y3A
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 45 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D GLU 3.2 1.6 - - - -
44D SER* 1.3 75.8 - - - +
46D LYS* 1.3 60.4 + - - +
48D THR* 3.2 4.2 + - - -
49D ILE* 3.1 30.4 + - - +
224D CYS* 4.9 1.3 - - - -
269D ASN* 4.0 3.1 - - - -
326D ALA* 4.3 0.3 - - - +
358D GDP 2.6 49.0 + - - -
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Residues in contact with LYS 46 (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 LEU* 3.5 28.0 - - + +
39D LEU 3.6 31.4 - - - +
40D GLY 3.3 8.7 + - - +
41D ALA 3.2 26.1 + - - -
42D GLY* 4.0 2.2 - - - -
44D SER* 3.8 7.8 - - - +
45D GLY* 1.3 76.3 - - - +
47D SER* 1.3 59.2 + - - +
49D ILE* 3.2 4.1 + - - +
50D VAL* 3.1 22.7 + - - +
200D ASP* 3.3 29.4 - - - +
201D VAL 3.6 12.3 - - - +
202D GLY* 4.5 7.0 - - - -
224D CYS* 4.5 6.0 - - - -
358D GDP 2.8 37.3 + - - +
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Residues in contact with SER 47 (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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45D GLY 3.5 0.2 - - - -
46D LYS* 1.3 74.4 - - - +
48D THR* 1.3 60.5 + - - +
50D VAL* 3.3 8.8 + - - +
51D LYS* 3.0 42.9 + - - +
179D VAL 4.9 2.6 + - - -
181D THR* 3.6 24.0 - - - -
200D ASP* 3.4 10.7 + - - -
358D GDP 2.9 36.7 + - - -
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Residues in contact with THR 48 (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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45D GLY 3.5 4.7 - - - -
46D LYS 3.2 0.2 - - - -
47D SER* 1.3 74.8 + - - +
49D ILE* 1.3 66.5 + - - +
51D LYS* 3.2 12.8 + - - +
52D GLN* 3.0 21.0 + - - +
175D LEU* 3.8 18.0 + - + +
177D THR 5.1 0.5 + - - -
326D ALA* 3.4 34.1 - - + +
327D THR* 3.9 16.6 - - + -
358D GDP 2.6 45.7 + - + -
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Residues in contact with ILE 49 (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 LEU* 4.2 20.6 - - + -
45D GLY 3.1 14.2 + - - +
46D LYS 3.2 7.4 + - - +
48D THR* 1.3 73.5 - - - +
50D VAL* 1.3 65.7 + - - +
52D GLN* 2.9 9.6 + - - +
53D MET* 2.9 39.4 + - + +
198D MET* 4.7 4.9 - - + -
222D ILE* 6.0 1.3 - - + -
224D CYS* 3.9 20.2 - - - -
267D PHE* 3.3 40.4 - - + -
269D ASN* 5.6 2.0 - - - +
324D THR* 5.5 1.3 - - - +
326D ALA* 4.0 19.5 - - + -
332D VAL* 5.0 9.6 - - + -
336D PHE* 5.9 2.2 - - + -
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Residues in contact with VAL 50 (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 LEU* 3.8 16.4 - - + -
46D LYS 3.1 14.8 + - - +
47D SER* 3.4 9.6 - - - +
48D THR 3.2 0.4 - - - -
49D ILE* 1.3 77.2 - - - +
51D LYS* 1.3 63.7 + - + +
53D MET* 3.1 11.7 + - - +
54D LYS* 3.1 44.4 + - - +
185D VAL* 4.9 14.4 - - + +
187D THR* 4.1 17.7 - - + -
198D MET* 4.7 7.9 - - + +
200D ASP* 3.8 21.5 - - + +
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Residues in contact with LYS 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D SER* 3.0 39.7 + - - +
48D THR* 3.4 13.2 + - - +
50D VAL* 1.3 76.9 - - + +
52D GLN* 1.3 58.1 + - - +
54D LYS* 3.2 8.3 + - + +
55D ILE* 2.9 32.5 + - - +
61D TYR* 3.3 28.5 - - + +
69D TYR* 4.3 18.8 - - - -
174D VAL* 3.9 28.5 - - + +
175D LEU* 3.9 22.4 + - + +
177D THR* 4.2 14.4 + - - -
179D VAL* 6.2 2.6 - - - +
358D GDP 5.0 0.2 + - - -
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Residues in contact with GLN 52 (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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48D THR 3.0 15.1 + - - +
49D ILE* 2.9 10.8 + - - +
51D LYS* 1.3 74.5 - - - +
53D MET* 1.3 58.4 + - - +
55D ILE* 3.0 9.5 + - - +
56D ILE* 2.7 40.7 + - + +
175D LEU* 3.6 11.6 - - + +
326D ALA 2.8 29.8 + - - +
327D THR 3.3 10.1 + - - -
328D ASP 3.4 0.8 + - - -
329D THR* 2.9 55.9 - - - +
332D VAL* 3.7 23.8 - - + -
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Residues in contact with MET 53 (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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49D ILE* 2.9 22.1 + - + +
50D VAL* 3.4 8.7 - - - +
52D GLN* 1.3 75.9 - - - +
54D LYS* 1.3 59.5 + - - +
56D ILE* 4.4 7.4 - - + -
57D HIS* 2.8 42.0 + - + +
58D GLU* 3.6 6.5 + - - +
187D THR* 4.7 3.4 - - + -
189D PHE* 3.8 36.1 - - + -
198D MET* 3.9 24.5 - - + -
332D VAL* 3.8 29.2 - - + -
336D PHE* 3.9 36.8 - - + -
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Residues in contact with LYS 54 (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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50D VAL* 3.1 32.5 + - - +
51D LYS* 3.4 8.4 - - - +
52D GLN 3.1 0.2 - - - -
53D MET* 1.3 76.8 - - - +
55D ILE* 1.3 61.2 + - - +
58D GLU* 3.1 44.1 + - + +
60D GLY* 2.9 22.3 + - - +
61D TYR* 3.9 26.7 + - + +
185D VAL* 5.7 5.6 - - - +
186D GLU 5.7 1.6 - - - -
187D THR* 3.9 11.7 - - - +
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Residues in contact with ILE 55 (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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51D LYS 2.9 17.8 + - - +
52D GLN* 3.0 26.7 + - - +
54D LYS* 1.3 79.3 - - - +
56D ILE* 1.3 63.0 + - + +
59D ALA* 4.4 3.1 + - - -
60D GLY* 3.2 14.9 + - - -
61D TYR* 3.5 26.5 - - + -
171D GLN* 3.5 36.8 - - + +
175D LEU* 4.0 26.2 - - + -
329D THR* 4.6 12.8 - - + +
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Residues in contact with ILE 56 (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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52D GLN* 2.7 26.0 + - + +
53D MET* 4.4 4.7 - - + -
55D ILE* 1.3 76.1 - - + +
57D HIS* 1.3 86.7 + - + +
58D GLU 3.7 0.6 + - - -
59D ALA 5.4 0.3 + - - -
329D THR* 3.7 21.1 - - - +
332D VAL* 4.1 14.8 - - + -
333D GLN* 3.5 58.3 - - + +
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Residues in contact with HIS 57 (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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53D MET* 2.8 28.1 + - + +
56D ILE* 1.3 100.8 - - + +
58D GLU* 1.3 64.5 + - - +
59D ALA 4.0 0.4 - - - -
189D PHE* 3.8 32.6 - + + +
190D THR 4.4 9.7 + - - +
191D PHE* 3.4 46.5 - + + -
333D GLN* 5.9 1.3 - - + +
336D PHE* 3.7 31.9 - + + -
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Residues in contact with GLU 58 (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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53D MET 4.1 0.3 - - - -
54D LYS* 3.1 41.7 + - + +
56D ILE 3.7 0.2 - - - -
57D HIS* 1.3 84.9 - - - +
59D ALA* 1.3 71.2 + - - +
60D GLY 3.5 0.4 - - - -
187D THR* 2.8 25.4 + - - -
188D HIS 3.0 25.7 + - - +
189D PHE* 3.8 14.2 - - + +
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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