Contacts of the strand formed by residues 114 - 126 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99D SER* 3.3 7.2 - - - +
102D GLN* 3.3 31.9 - - - +
64F PHE* 3.7 5.8 - - + -
65F SER* 3.0 39.2 - - - -
66F GLY* 3.1 39.5 + - - -
68F GLY 2.8 32.0 + - - -
69F CYS* 4.4 0.2 - - - -
70F PRO* 6.2 0.7 - - + -
74F VAL* 5.4 3.6 - - + -
76F LEU* 3.6 25.4 - - + -
100F PRO* 3.5 33.0 - - + -
101F CYS* 4.1 12.1 - - - -
112F ASN 4.5 0.7 - - - -
113F PRO* 1.3 74.0 - - - +
115F TYR* 1.3 67.2 - - - +
116F GLU* 3.8 8.5 - - + +
141F TYR* 3.9 26.5 - + - -
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Residues in contact with TYR 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D LEU* 3.8 31.6 - - + -
97D ILE* 3.6 55.6 - - + +
98D ARG* 3.1 32.6 + - - +
99D SER* 3.1 6.3 + - - -
63F LEU* 4.7 7.9 - - + -
64F PHE 3.3 6.5 - - - +
65F SER* 3.5 17.5 - - - -
113F PRO* 4.0 14.7 - - + +
114F TRP* 1.3 79.1 - - - +
116F GLU* 1.3 63.2 + - - +
117F PRO* 4.1 1.1 - - - -
143F ASP* 3.5 22.6 + - - -
113W ARG* 4.2 13.9 + - - +
114W LEU* 4.5 18.5 - - - +
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Residues in contact with GLU 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ARG* 3.3 31.1 + - - -
102D GLN* 5.4 2.6 + - - -
63F LEU* 3.7 3.3 - - - +
64F PHE* 2.9 43.3 + - + -
76F LEU* 4.1 13.9 - - + -
98F ARG* 3.0 45.2 + - + +
100F PRO* 3.5 44.5 - - + +
114F TRP* 3.8 4.7 - - + +
115F TYR* 1.3 79.7 + - - +
117F PRO* 1.3 64.9 - - - +
118F ILE* 5.1 0.7 - - + -
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Residues in contact with PRO 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ALA* 4.1 18.2 - - + -
97D ILE 3.0 27.1 - - - +
98D ARG* 3.7 20.6 - - + -
118D ILE* 5.0 8.7 - - + -
117E PRO* 5.9 1.0 - - - +
61F GLN* 5.1 5.8 - - - +
62F VAL 3.5 9.0 - - - +
63F LEU* 3.5 12.6 - - + -
98F ARG* 5.2 5.0 - - - +
116F GLU* 1.3 86.6 - - - +
118F ILE* 1.3 64.7 - - - +
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Residues in contact with ILE 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E PRO* 5.0 7.6 - - + -
61F GLN* 3.4 7.9 - - - +
62F VAL* 3.1 36.9 + - + +
64F PHE* 4.2 19.1 - - + -
76F LEU 3.8 15.5 - - - +
78F HIS* 3.9 27.3 - - + +
96F ALA* 3.4 32.3 - - + +
97F ILE 4.4 1.3 - - - -
98F ARG* 3.8 31.9 - - + +
116F GLU 4.0 1.5 + - - +
117F PRO* 1.3 79.1 - - - +
119F TYR* 1.3 67.6 + - - +
120F LEU* 4.4 1.6 - - + -
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Residues in contact with TYR 119 (chain F).
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* 6.0 0.3 - - - +
119D TYR* 3.9 32.2 - + + +
121D GLY* 2.7 31.9 + - - -
61E GLN* 3.4 10.6 - - - +
117E PRO* 5.8 2.5 - - - +
119E TYR* 3.9 48.8 - + + +
59F TYR* 3.6 13.5 - - + +
60F SER 3.6 4.9 - - - -
61F GLN* 3.8 12.3 - - + +
96F ALA* 4.9 0.3 - - - +
118F ILE* 1.3 77.5 - - - +
120F LEU* 1.3 103.8 + - - +
121F GLY* 4.1 2.0 - - - -
151F TYR* 3.3 31.6 - + - -
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Residues in contact with LEU 120 (chain F).
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* 3.5 15.7 - - - +
151E TYR* 3.9 4.0 - - - -
59F TYR* 3.3 1.2 - - - -
60F SER 3.0 30.9 + - - +
78F HIS* 3.3 46.0 - - + +
80F ILE* 3.9 15.3 - - + +
94F LEU* 3.7 33.0 - - + +
95F SER 3.5 27.6 - - - +
96F ALA* 3.7 9.4 - - + -
118F ILE* 4.4 0.7 - - + -
119F TYR* 1.3 95.2 - - - +
121F GLY* 1.3 58.5 - - - +
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Residues in contact with GLY 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E TYR* 4.1 0.9 - - - -
119E TYR* 3.1 25.5 + - - -
151E TYR* 3.1 27.1 + - - -
57F LEU* 5.2 2.0 - - - -
58F ILE 3.1 12.1 - - - -
59F TYR* 4.0 7.0 - - - -
94F LEU* 3.4 8.6 - - - +
119F TYR* 4.2 1.8 - - - -
120F LEU* 1.3 76.4 - - - +
122F GLY* 1.3 58.0 + - - -
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Residues in contact with GLY 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E HIS* 4.1 3.8 - - - -
59E TYR* 3.6 17.9 - - - -
56F TYR 3.7 0.3 - - - +
57F LEU* 3.5 8.4 - - - +
58F ILE* 2.8 34.4 + - - +
94F LEU* 3.8 2.3 - - - +
121F GLY* 1.3 75.0 - - - -
123F VAL* 1.3 63.2 + - - -
124F PHE* 3.7 14.9 - - - -
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Residues in contact with VAL 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E VAL* 4.2 24.2 - - + -
15E HIS* 3.5 22.7 + - + +
34E ASN 4.7 0.2 - - - +
36E LEU* 4.2 6.6 - - + +
57E LEU* 4.9 0.2 - - + -
59E TYR* 2.7 35.2 + - + +
154E ILE 5.5 0.4 - - - +
155E ILE* 4.0 30.5 - - + -
55F LEU* 4.4 12.8 - - + -
56F TYR 3.2 11.2 - - - +
57F LEU* 3.9 16.2 - - + -
122F GLY* 1.3 72.4 - - - -
124F PHE* 1.3 74.3 + - - +
157F LEU* 4.6 3.1 - - + -
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Residues in contact with PHE 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E HIS* 3.8 17.5 - + - -
34E ASN* 3.4 32.1 - - + +
36E LEU* 4.4 3.6 - - - -
55F LEU* 3.4 7.6 - - - -
56F TYR* 2.8 35.2 + - - +
58F ILE* 3.3 29.8 - - + -
93F LEU* 3.6 42.4 - - + -
94F LEU* 3.6 36.8 - - + -
122F GLY 3.7 20.4 - - - -
123F VAL* 1.3 75.1 - - - +
125F GLN* 1.3 62.7 + - - +
126F LEU* 3.8 9.9 + - + -
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Residues in contact with GLN 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E SER 4.9 7.0 + - - -
34E ASN* 5.8 2.8 + - - +
36E LEU* 4.3 17.0 - - + +
53F GLU* 3.7 18.4 + - - +
54F GLY* 3.4 12.9 - - - +
55F LEU* 3.8 20.6 - - + +
82F ARG* 3.4 20.4 + - - +
124F PHE* 1.3 74.9 - - - +
126F LEU* 1.3 70.6 + - - +
127F GLU* 3.7 22.2 + - - +
69V PRO* 6.3 4.0 - - + -
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Residues in contact with LEU 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F VAL* 3.5 31.2 - - + -
52F SER 3.8 0.8 - - - +
53F GLU* 3.2 18.4 - - - -
54F GLY 3.0 12.3 + - - -
56F TYR* 3.6 41.7 - - + -
58F ILE* 4.1 14.8 - - + -
82F ARG* 3.9 23.6 - - + +
93F LEU* 5.2 0.7 - - + -
124F PHE* 4.3 7.0 - - + +
125F GLN* 1.3 84.2 - - - +
127F GLU* 1.3 74.3 + - - +
130F ASP* 3.7 3.4 - - - +
132F LEU* 3.8 26.0 - - + -
154F ILE* 5.2 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