Contacts of the strand formed by residues 114 - 126 (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 TRP 114 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E PHE* 3.8 13.9 - - + -
65E SER* 3.0 39.8 - - - -
66E GLY* 2.9 37.4 + - - -
68E GLY 3.3 21.6 + - - -
69E CYS* 3.9 13.8 - - - -
70E PRO* 6.0 0.9 - - + -
74E VAL* 5.5 4.0 - - + -
76E LEU* 4.0 6.1 - - + -
100E PRO* 3.8 35.9 - - + -
101E CYS* 4.6 4.5 - - - -
112E ASN 4.1 9.0 - - - -
113E PRO* 1.3 74.9 - - - +
115E TYR* 1.3 68.2 + - - +
116E GLU* 3.9 8.5 - - + +
141E TYR* 3.3 37.0 - + - -
98F ARG* 5.6 1.1 - - - +
99F SER* 3.3 10.1 - - - +
102F GLN* 3.6 26.7 - - - +
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Residues in contact with TYR 115 (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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63E LEU* 4.6 5.4 - - + -
64E PHE 3.2 5.2 - - - +
65E SER* 3.7 16.6 - - - -
113E PRO* 4.0 22.2 - - + +
114E TRP* 1.3 80.4 - - - +
116E GLU* 1.3 63.3 + - - +
143E ASP* 3.4 21.8 - - - -
75F LEU* 4.4 22.7 - - + -
97F ILE* 3.4 52.1 - - + +
98F ARG* 3.0 27.8 + - - +
99F SER* 3.4 5.3 + - - -
106V LEU* 5.3 0.4 - - + -
113V ARG* 3.9 23.8 + - - +
114V LEU* 4.0 24.7 - - + +
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Residues in contact with GLU 116 (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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63E LEU* 3.6 4.6 - - - +
64E PHE* 2.8 51.0 + - + -
76E LEU* 4.3 3.8 - - + -
98E ARG* 2.9 50.7 + - + +
100E PRO* 3.8 23.7 - - + +
114E TRP* 3.9 18.0 - - + +
115E TYR* 1.3 79.9 - - - +
117E PRO* 1.3 67.8 - - - +
98F ARG* 3.2 29.1 + - - -
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Residues in contact with PRO 117 (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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117D PRO* 5.8 1.2 - - - +
61E GLN* 5.0 6.3 - - - +
62E VAL 3.5 9.4 - - - +
63E LEU* 3.6 10.3 - - + -
98E ARG* 5.0 3.8 - - - -
116E GLU* 1.3 90.4 - - - +
118E ILE* 1.3 67.5 + - - +
119E TYR 4.3 0.4 - - - +
96F ALA* 4.1 19.5 - - + -
97F ILE 3.2 24.9 - - - +
98F ARG* 3.6 21.5 - - + -
117F PRO 5.9 0.9 - - - +
118F ILE* 5.0 9.4 - - + -
119F TYR 5.8 2.0 - - - +
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Residues in contact with ILE 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D PRO* 5.1 7.2 - - + -
61E GLN* 3.3 6.8 - - - +
62E VAL* 3.2 32.1 + - + -
64E PHE* 3.9 21.8 - - + -
76E LEU 3.8 14.4 - - - +
78E HIS* 3.7 33.5 - - + -
96E ALA* 3.5 32.8 - - + +
97E ILE 4.5 1.3 - - - -
98E ARG* 3.8 28.9 - - + +
116E GLU 4.7 1.1 - - - +
117E PRO* 1.3 81.7 - - - +
119E TYR* 1.3 62.7 + - - +
120E LEU* 4.0 3.8 - - + -
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Residues in contact with TYR 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D GLN* 3.5 8.8 - - - +
117D PRO* 6.0 1.4 - - - +
119D TYR* 3.8 45.2 + + + +
59E TYR* 3.3 18.9 - - + +
60E SER 3.6 10.3 - - - -
61E GLN* 3.8 6.5 - - + +
96E ALA* 5.3 0.5 - - - +
117E PRO 4.3 0.2 - - - -
118E ILE* 1.3 74.9 - - - +
120E LEU* 1.3 103.1 + - - +
121E GLY* 4.1 1.1 - - - -
151E TYR* 3.6 22.2 - + - -
57F LEU* 5.9 1.0 - - - +
119F TYR* 3.9 38.7 - + + +
121F GLY* 3.1 39.1 + - - -
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Residues in contact with LEU 120 (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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61D GLN* 3.5 14.1 - - - +
119D TYR* 4.6 0.2 - - - -
151D TYR* 3.9 3.6 - - - -
59E TYR* 3.1 2.3 - - - -
60E SER 2.9 33.0 + - - +
78E HIS* 3.3 45.8 - - + +
80E ILE* 4.1 13.5 - - + +
94E LEU* 3.6 35.4 - - + +
95E SER 3.8 9.2 - - - +
96E ALA* 3.7 25.4 - - + -
118E ILE* 4.0 2.9 - - + -
119E TYR* 1.3 94.5 - - - +
121E GLY* 1.3 57.0 + - - +
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Residues in contact with GLY 121 (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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59D TYR* 3.4 1.6 - - - -
119D TYR* 2.9 34.7 + - - -
151D TYR* 3.3 19.6 + - - -
57E LEU* 5.0 3.1 - - - -
58E ILE 3.1 11.7 - - - -
59E TYR* 4.1 4.5 - - - -
94E LEU* 3.5 7.4 - - - +
119E TYR* 4.2 3.6 - - - -
120E LEU* 1.3 76.0 - - - +
122E GLY* 1.3 58.7 + - - -
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Residues in contact with GLY 122 (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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15D HIS* 4.2 2.9 - - - -
59D TYR* 3.3 19.3 - - - -
57E LEU* 4.1 6.6 - - - +
58E ILE 2.9 28.8 + - - +
94E LEU* 4.0 2.4 - - - +
121E GLY* 1.3 75.5 - - - -
123E VAL* 1.3 63.1 + - - -
124E PHE* 3.3 20.5 - - - -
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Residues in contact with VAL 123 (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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13D VAL* 4.0 19.1 - - + -
14D ALA 5.3 0.4 - - - +
15D HIS* 3.6 21.5 + - - +
36D LEU* 4.2 4.7 - - + +
57D LEU* 5.2 0.2 - - + -
59D TYR* 2.7 27.9 + - + +
154D ILE 5.5 0.2 - - - +
155D ILE* 3.7 47.8 - - + -
55E LEU* 4.2 15.9 - - + -
56E TYR 3.6 9.4 - - - +
57E LEU* 4.5 12.8 - - + +
122E GLY* 1.3 73.0 - - - -
124E PHE* 1.3 71.1 + - - +
157E LEU* 4.5 4.0 - - + -
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Residues in contact with PHE 124 (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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15D HIS* 3.7 18.4 - + - -
34D ASN* 3.6 31.0 - - + -
36D LEU* 4.4 2.9 - - - -
55E LEU* 3.4 5.8 - - - -
56E TYR* 2.7 40.0 + - - +
58E ILE* 3.9 26.5 - - + -
82E ARG* 6.3 0.2 - - - -
93E LEU* 3.5 57.2 - - + -
94E LEU* 3.9 20.0 - - + -
122E GLY* 3.3 32.8 - - - -
123E VAL* 1.3 75.4 - - - +
125E GLN* 1.3 66.4 + - - +
126E LEU* 4.5 4.3 - - + -
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Residues in contact with GLN 125 (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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34D ASN* 4.7 3.8 - - - +
36D LEU* 4.1 19.7 - - + +
53E GLU* 5.0 9.1 + - - -
54E GLY* 3.9 8.8 - - - +
55E LEU* 3.9 22.7 - - + +
82E ARG* 3.8 15.7 + - - +
124E PHE* 1.3 73.7 - - - +
126E LEU* 1.3 81.9 + - - +
127E GLU* 3.7 19.0 + - + +
44U PHE* 6.2 1.6 - - - -
69U PRO* 5.2 13.1 - - + +
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Residues in contact with LEU 126 (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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50E VAL* 3.5 29.8 - - + -
52E SER 4.7 0.7 - - - -
53E GLU* 3.2 21.9 - - - +
54E GLY 3.2 11.1 + - - -
56E TYR* 3.8 28.3 - - + -
58E ILE* 3.8 13.7 - - + -
82E ARG* 3.5 32.3 - - + +
93E LEU* 5.0 0.9 - - + -
124E PHE* 4.2 13.2 - - + +
125E GLN* 1.3 86.2 - - - +
127E GLU* 1.3 72.4 + - - +
130E ASP* 3.5 5.4 - - - +
132E LEU* 3.6 22.0 - - + -
154E ILE* 5.5 0.2 - - + -
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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