Contacts of the strand formed by residues 54 - 66 (chain D) in PDB entry 3ALQ
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 54 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D SER 4.0 0.6 + - - -
53D GLU* 1.3 80.9 - - - +
55D LEU* 1.3 65.6 + - - -
56D TYR* 3.6 10.0 - - - -
124D PHE 3.6 0.3 - - - +
125D GLN* 3.4 5.8 - - - -
126D LEU 2.8 38.3 + - - +
156D ALA* 5.8 2.7 - - - -
157D LEU* 5.9 0.4 - - - -
9F SER 5.7 5.6 - - - -
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Residues in contact with LEU 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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54D GLY* 1.3 69.2 - - - -
56D TYR* 1.3 61.4 + - - +
123D VAL* 4.0 9.6 - - + -
124D PHE 3.6 2.9 - - - -
125D GLN* 3.6 38.8 - - + +
156D ALA* 3.7 1.9 - - - +
157D LEU* 3.0 37.4 + - + +
9F SER* 3.5 36.3 - - - +
11F MET 4.9 0.7 - - - +
13F VAL* 3.7 35.0 - - + -
36F LEU* 3.8 19.5 - - + -
39F ASN* 5.5 0.4 - - - +
155F ILE* 4.0 11.2 - - + -
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Residues in contact with TYR 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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12D PRO* 3.7 16.1 - - + +
50D VAL* 3.4 17.4 - - + +
51D PRO* 3.5 10.4 - - + +
52D SER* 3.1 39.3 + - - -
53D GLU 4.5 0.2 - - - -
54D GLY* 3.6 20.6 - - - -
55D LEU* 1.3 75.0 - - - +
57D LEU* 1.3 61.8 + - - +
58D ILE* 3.6 8.7 + - + +
122D GLY 3.6 0.9 - - - +
123D VAL* 3.2 4.8 - - - -
124D PHE* 2.7 40.0 + - - +
126D LEU* 3.5 32.3 - - + -
154D ILE* 3.9 26.2 - - + -
155D ILE 3.4 6.3 - - - +
156D ALA* 3.5 35.0 - - + -
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Residues in contact with LEU 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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55D LEU 4.1 1.2 + - - -
56D TYR* 1.3 71.8 - - - +
58D ILE* 1.3 70.4 + - - +
59D TYR* 4.3 15.9 - - + -
121D GLY* 4.7 1.8 - - - -
122D GLY* 3.6 22.2 - - - +
123D VAL* 4.4 4.3 - - + +
153D GLY 3.7 1.0 - - - +
154D ILE* 3.1 6.8 - - - -
155D ILE* 2.8 49.6 + - + +
157D LEU* 3.9 18.7 - - + +
57E LEU* 4.1 26.5 - - + -
123E VAL* 5.2 0.2 - - + -
157E LEU* 5.3 2.7 - - + -
57F LEU* 4.0 28.9 - - + -
59F TYR* 5.7 0.4 - - + -
119F TYR* 6.0 0.4 - - - +
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Residues in contact with ILE 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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56D TYR* 4.0 11.0 - - + +
57D LEU* 1.3 78.3 - - - +
59D TYR* 1.3 63.8 - - - +
80D ILE* 3.7 31.2 - - + -
93D LEU* 4.3 4.0 - - + -
94D LEU* 3.5 3.5 - - + +
121D GLY* 2.8 3.6 - - - -
122D GLY 2.8 39.6 + - - +
124D PHE* 3.8 26.0 - - + -
126D LEU* 3.9 13.2 - - + -
132D LEU* 3.7 31.2 - - + -
152D PHE* 4.1 4.7 - - + -
153D GLY 3.5 8.3 - - - +
154D ILE* 4.0 15.7 - - + -
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Residues in contact with TYR 59 (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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14D ALA 3.9 2.8 + - - -
15D HIS* 2.9 22.9 + - - -
57D LEU* 4.3 22.0 - - + -
58D ILE* 1.3 77.4 - - - +
60D SER* 1.3 64.7 + - - +
80D ILE* 3.8 3.1 - - - -
119D TYR* 3.2 20.9 - - + +
120D LEU 2.9 10.3 - - - +
121D GLY* 3.8 3.4 - - - -
151D TYR* 3.9 13.9 - + - -
152D PHE* 3.5 2.3 - - - -
153D GLY* 2.9 58.9 + - - +
154D ILE* 4.3 2.0 - - - -
57E LEU* 5.6 1.8 - - + -
121E GLY 3.4 14.1 - - - -
122E GLY* 3.3 14.8 - - - -
123E VAL* 2.7 49.3 + - + +
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Residues in contact with SER 60 (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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28D TRP* 4.5 1.4 - - - -
59D TYR* 1.3 79.5 - - - +
61D GLN* 1.3 58.3 + - - +
78D HIS* 3.1 27.5 + - - -
80D ILE* 3.4 22.9 - - - -
118D ILE 3.9 0.3 - - - +
119D TYR* 3.4 3.9 - - - -
120D LEU* 2.7 35.3 + - - +
134D ALA* 3.8 8.5 - - - +
151D TYR* 2.9 24.4 + - - -
152D PHE* 3.9 4.0 - - - +
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Residues in contact with GLN 61 (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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60D SER* 1.3 74.8 + - - +
62D VAL* 1.3 81.0 + - - +
63D LEU* 4.8 3.6 - - - +
78D HIS* 4.1 0.4 - - - -
117D PRO* 5.1 3.7 - - - +
118D ILE 3.3 13.7 - - - +
119D TYR* 4.0 6.0 - - + -
148D GLY 3.8 0.8 + - - -
149D GLN* 3.1 18.3 + - - +
150D VAL* 3.5 2.6 - - - +
151D TYR* 2.7 71.9 + - + +
95E SER 2.9 26.5 + - - -
96E ALA* 4.1 8.6 - - - +
119E TYR 3.5 18.2 - - - +
120E LEU* 3.5 8.3 - - - +
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Residues in contact with VAL 62 (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 LEU* 5.1 6.7 - - + -
28D TRP* 5.2 1.1 - - + -
60D SER* 4.8 0.7 - - - +
61D GLN* 1.3 83.4 - - - +
63D LEU* 1.3 61.7 + - - +
64D PHE* 3.5 26.7 - - + -
78D HIS* 3.4 48.2 - - + +
117D PRO* 3.4 2.9 - - - +
118D ILE* 3.0 31.5 + - + -
136D ILE* 3.9 9.9 - - + -
142D LEU* 4.2 12.3 - - + -
149D GLN 3.8 6.1 - - - -
150D VAL* 4.2 14.6 - - + -
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Residues in contact with LEU 63 (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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61D GLN* 4.8 3.1 - - - +
62D VAL* 1.3 78.7 - - - +
64D PHE* 1.3 70.9 + - - +
115D TYR* 4.4 4.9 - - + -
116D GLU 3.3 29.6 - - - +
117D PRO* 3.4 16.4 - - + -
142D LEU* 3.6 4.2 - - - +
143D ASP* 3.0 31.4 + - + +
149D GLN* 3.2 56.2 + - + +
150D VAL* 4.3 3.9 - - - +
96E ALA* 4.6 2.7 - - - -
97E ILE* 3.8 22.4 - - + +
113U ARG* 4.1 8.1 - - - +
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Residues in contact with PHE 64 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62D VAL* 3.5 22.0 - - + -
63D LEU* 1.3 80.0 - - - +
65D SER* 1.3 62.6 + - - +
76D LEU* 3.7 47.6 - - + -
77D THR 4.1 10.5 - - - -
114D TRP* 3.7 7.2 - - + -
115D TYR* 3.4 1.2 - - - -
116D GLU* 2.7 46.0 + - + +
118D ILE* 4.3 13.2 - - + -
136D ILE* 3.9 33.4 - - + -
137D ASN* 4.8 0.9 - - - -
138D ARG* 3.6 18.8 - - + -
141D TYR* 3.0 30.5 - - + +
142D LEU* 4.1 3.6 - - + -
143D ASP* 4.5 0.2 - - - -
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Residues in contact with SER 65 (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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64D PHE* 1.3 78.3 - - - +
66D GLY* 1.3 59.2 + - - +
114D TRP* 3.1 21.8 - - - -
115D TYR* 3.5 20.0 + - - -
140D ASP 5.4 0.2 - - - +
141D TYR* 2.9 24.8 + - - +
142D LEU 4.8 2.4 + - - +
143D ASP* 2.7 28.8 + - - +
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Residues in contact with GLY 66 (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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65D SER* 1.3 76.2 - - - +
67D GLN* 1.3 64.0 + - - -
68D GLY 3.5 2.2 - - - -
113D PRO* 3.3 4.7 - - - +
114D TRP* 3.0 56.8 + - - +
141D TYR* 4.3 8.5 - - - -
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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