Contacts of the strand formed by residues 54 - 66 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D SER* 5.7 5.4 - - - -
53E GLU* 1.3 85.7 - - - +
55E LEU* 1.3 65.6 + - - -
56E TYR* 3.1 18.4 - - - -
125E GLN* 4.6 4.4 - - - +
126E LEU 3.2 16.3 + - - -
156E ALA* 6.0 1.6 - - - -
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Residues in contact with LEU 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D SER* 3.8 32.2 - - - +
11D MET* 4.9 0.9 - - + +
13D VAL* 3.8 37.0 - - + -
36D LEU* 3.8 26.2 - - + -
155D ILE* 4.3 14.8 - - + -
54E GLY* 1.3 74.7 - - - -
56E TYR* 1.3 60.3 + - - +
123E VAL* 4.2 7.2 - - + -
124E PHE 3.4 2.2 - - - +
125E GLN* 3.9 28.0 - - + +
156E ALA* 3.3 7.8 - - - +
157E LEU* 3.1 32.5 + - + +
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Residues in contact with TYR 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E PRO* 3.7 16.8 - - + +
50E VAL* 3.2 21.7 - - + +
51E PRO* 3.5 10.8 - - + +
52E SER* 2.7 36.1 + - - -
53E GLU 4.2 1.3 - - - -
54E GLY* 3.1 31.4 - - - -
55E LEU* 1.3 76.3 - - - +
57E LEU* 1.3 64.1 + - - +
58E ILE* 3.3 12.4 + - + +
123E VAL* 4.4 3.6 - - - -
124E PHE 2.7 34.1 + - - +
126E LEU* 3.8 25.8 - - + -
154E ILE* 4.2 21.3 - - + -
155E ILE 3.4 7.4 - - - -
156E ALA* 3.5 31.3 - - + +
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Residues in contact with LEU 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D LEU* 4.1 27.4 - - + -
59D TYR* 5.6 1.6 - - + -
119D TYR* 5.9 0.9 - - - +
56E TYR* 1.3 71.2 - - - +
58E ILE* 1.3 64.3 + - - +
59E TYR* 4.3 15.7 - - + -
121E GLY* 5.0 1.8 - - - -
122E GLY* 3.9 23.6 - - - +
123E VAL* 4.5 7.6 - - + +
153E GLY 4.0 0.5 - - - +
154E ILE* 3.1 7.6 - - - +
155E ILE* 3.0 47.1 + - + -
157E LEU* 4.0 22.2 - - + +
57F LEU* 3.8 31.0 - - + -
123F VAL* 4.9 0.2 - - + -
157F LEU* 5.4 1.3 - - + -
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Residues in contact with ILE 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E TYR* 3.5 13.5 - - + +
57E LEU* 1.3 79.1 - - - +
59E TYR* 1.3 62.1 + - - +
80E ILE* 3.9 31.2 - - + -
93E LEU* 4.1 11.2 - - + -
94E LEU* 3.4 6.1 - - + +
121E GLY* 3.1 3.8 - - - -
122E GLY 2.9 35.1 + - - +
124E PHE* 3.9 27.4 - - + -
126E LEU* 3.8 14.6 - - + -
132E LEU* 3.7 22.4 - - + -
152E PHE* 4.4 3.1 - - + -
153E GLY 3.7 2.5 - - - +
154E ILE* 3.8 19.1 - - + -
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Residues in contact with TYR 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E ALA 4.1 1.2 + - - -
15E HIS* 2.5 46.3 + + - +
57E LEU* 4.3 22.0 - - + -
58E ILE* 1.3 74.5 - - - +
60E SER* 1.3 66.9 + - - +
80E ILE* 3.9 4.0 - - - -
119E TYR* 3.3 22.4 - - - +
120E LEU 3.1 9.0 - - - +
121E GLY* 4.2 3.1 - - - -
151E TYR* 3.9 12.3 - + - -
152E PHE* 3.3 5.4 - - - -
153E GLY* 2.9 56.6 + - - +
154E ILE* 4.5 2.9 - - - -
57F LEU* 5.2 1.3 - - + -
121F GLY 4.1 4.9 - - - -
122F GLY* 3.6 6.7 - - - -
123F VAL* 2.7 45.2 + - + +
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Residues in contact with SER 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E TRP* 4.2 2.8 - - - -
59E TYR* 1.3 84.4 - - - +
61E GLN* 1.3 61.0 + - - +
78E HIS* 3.2 25.5 + - - -
80E ILE* 3.6 19.1 - - - -
118E ILE 3.9 0.5 - - - +
119E TYR* 3.6 5.8 - - - -
120E LEU* 2.9 32.4 + - - +
134E ALA* 4.2 0.9 - - - +
151E TYR* 2.8 22.6 + - - -
152E PHE* 3.8 11.6 - - - +
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Residues in contact with GLN 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E SER* 1.3 73.9 + - - +
62E VAL* 1.3 81.8 + - - +
63E LEU* 5.3 1.4 - - - +
78E HIS* 4.2 0.4 - - - -
117E PRO* 5.0 4.1 - - + +
118E ILE 3.3 14.1 - - - +
119E TYR* 3.8 6.8 - - + +
148E GLY 3.4 6.1 + - - -
149E GLN* 2.9 23.5 + - - +
150E VAL* 3.4 1.2 - - - +
151E TYR* 3.1 63.7 + - + +
95F SER 2.9 25.4 + - - -
96F ALA* 4.2 7.8 - - - +
119F TYR 3.4 20.1 - - - +
120F LEU* 3.5 7.5 - - - +
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Residues in contact with VAL 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E LEU* 4.6 7.0 - - + -
28E TRP* 4.9 1.1 - - + -
60E SER* 4.7 0.9 - - - +
61E GLN* 1.3 86.8 - - - +
63E LEU* 1.3 63.5 + - - +
64E PHE* 3.7 30.3 - - + -
78E HIS* 3.4 42.0 - - + +
117E PRO* 3.5 3.1 - - - +
118E ILE* 3.2 29.4 + - + -
136E ILE* 4.2 8.5 - - + -
142E LEU* 4.1 12.6 - - + -
149E GLN 3.6 7.4 - - - -
150E VAL* 3.9 14.8 - - + -
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Residues in contact with LEU 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E GLN* 5.3 1.3 - - - +
62E VAL* 1.3 77.1 - - - +
64E PHE* 1.3 67.8 + - - +
115E TYR* 4.6 4.0 - - + -
116E GLU 3.6 7.6 - - - +
117E PRO* 3.5 39.9 - - + -
142E LEU* 3.3 9.4 - - - +
143E ASP* 3.0 40.5 + - + +
149E GLN* 3.4 48.0 - - + +
150E VAL* 3.7 5.9 - - - +
96F ALA* 4.7 3.1 - - + -
97F ILE* 4.0 25.1 - - + +
113V ARG* 4.0 8.7 - - - +
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Residues in contact with PHE 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E VAL* 3.7 18.6 - - + -
63E LEU* 1.3 79.8 - - - +
65E SER* 1.3 61.8 + - - +
76E LEU* 3.4 58.1 - - + -
77E THR 4.4 4.5 - - - -
114E TRP* 3.8 6.5 - - + -
115E TYR* 3.2 5.5 - - - +
116E GLU* 2.8 48.7 + - + +
118E ILE* 3.9 15.5 - - + -
136E ILE* 3.9 36.3 - - + -
137E ASN* 4.7 0.4 - - - -
138E ARG* 3.7 18.6 - - + -
141E TYR* 3.1 22.0 - - + +
142E LEU* 4.2 2.7 - - + -
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Residues in contact with SER 65 (chain E).
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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63E LEU 4.4 0.2 + - - -
64E PHE* 1.3 76.3 - - - +
66E GLY* 1.3 60.3 + - - +
114E TRP* 3.0 18.2 - - - -
115E TYR* 3.7 15.7 - - - -
141E TYR* 2.8 26.4 + - - +
142E LEU 4.2 3.8 + - - +
143E ASP* 3.2 31.9 + - - +
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Residues in contact with GLY 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E SER* 1.3 75.9 - - - +
67E GLN* 1.3 62.3 + - - -
68E GLY 3.3 2.9 - - - -
113E PRO* 3.2 4.0 - - - +
114E TRP* 2.9 54.7 + - - -
115E TYR* 5.6 0.3 - - - -
141E TYR* 4.4 7.4 - - - -
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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