Contacts of the strand formed by residues 62 - 69 (chain A) in PDB entry 3Q8A
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 SER 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A TYR* 3.9 0.2 - - - -
24A PHE* 2.8 30.5 + - - +
26A ASP 2.5 23.0 + - - -
27A LEU 2.9 28.6 - - - -
28A ASN 3.1 2.8 + - - -
29A PHE* 3.2 19.6 + - - -
60A PHE* 3.4 3.6 - - - +
61A GLN* 1.3 76.8 - - - +
63A ALA* 1.3 64.7 + - - +
120A TYR* 2.9 19.1 - - - -
121A GLN* 3.5 2.2 - - - -
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A TYR 3.1 17.3 - - - +
23A TYR* 3.8 14.8 - - + -
24A PHE* 3.8 4.8 - - - -
29A PHE* 4.3 0.6 - - - -
60A PHE* 5.2 0.7 - - + -
62A SER* 1.3 78.3 - - - +
64A ILE* 1.3 62.6 + - - +
65A TRP* 3.4 26.6 - - + -
119A GLN* 3.4 3.1 - - - -
120A TYR* 2.8 35.9 + - + +
130A LEU* 4.1 6.5 - - + -
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU 4.4 0.4 - - - -
22A TYR* 2.7 49.4 + - + +
24A PHE* 3.8 13.2 - - + -
29A PHE* 3.3 50.3 - - + -
63A ALA* 1.3 72.6 - - - +
65A TRP* 1.3 78.4 + - - +
66A SER* 5.0 3.8 - - - +
117A LYS* 4.6 15.9 - - + -
118A ILE 3.1 12.3 - - - +
119A GLN* 4.8 4.3 - - + -
176A PRO* 5.5 8.3 - - + -
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Residues in contact with TRP 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.6 8.2 - - + +
20A LEU 3.2 7.9 - - - -
21A GLY* 3.1 27.9 - - - -
23A TYR* 3.1 42.5 + + - -
43A LEU* 3.4 42.0 - - + +
63A ALA* 3.4 22.4 - - + -
64A ILE* 1.3 88.9 - - - +
66A SER* 1.3 62.5 + - - +
116A ILE 3.4 1.8 - - - +
117A LYS* 3.4 5.9 - - - +
118A ILE* 2.7 68.2 + - + +
120A TYR* 3.7 15.5 - - + -
130A LEU* 3.4 22.4 - - + -
132A PHE* 4.1 14.8 - + - -
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Residues in contact with SER 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.6 5.8 - - - +
20A LEU* 2.9 37.7 + - - +
64A ILE* 5.4 4.0 - - - -
65A TRP* 1.3 76.2 - - - +
67A GLY* 1.3 60.5 + - - +
116A ILE 3.3 6.1 + - - -
117A LYS* 4.8 9.6 - - - +
154A PRO* 3.4 28.1 - - - +
167A ARG 6.1 1.2 - - - -
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Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.4 10.7 - - - +
66A SER* 1.3 79.7 + - - +
68A PHE* 1.3 61.2 + - - -
115A GLN* 3.4 3.7 - - - +
116A ILE* 2.6 41.4 + - - +
152A GLN 3.5 6.3 - - - -
154A PRO* 3.7 16.6 - - - +
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Residues in contact with PHE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.0 7.1 - - - +
67A GLY* 1.3 73.5 - - - -
69A ILE* 1.3 67.4 + - - +
113A LEU* 4.4 13.5 - - + -
114A TYR* 2.9 12.8 - - - -
115A GLN* 3.1 44.0 - - + -
116A ILE* 3.3 8.3 - - - +
151A LEU* 4.1 4.7 - - - +
152A GLN* 3.1 26.8 + - + +
153A LEU 3.5 9.2 - - - -
154A PRO* 4.5 2.5 - - + -
155A GLU 4.2 7.9 - - - -
163A SER 5.3 2.0 - - - -
164A ARG* 3.1 67.8 - - + +
165A LYS* 3.3 31.6 - - + -
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A PHE* 1.3 82.6 - - - +
70A LYS* 1.3 64.0 + - - +
71A VAL* 5.1 2.0 - - + -
79A PHE* 3.6 32.5 - - + -
91A VAL* 5.2 1.3 - - + -
108A LEU* 5.0 6.1 - - + -
113A LEU* 3.1 8.7 - - - +
114A TYR* 2.9 46.9 + - + +
116A ILE* 3.3 25.1 - - + -
136A TRP* 3.8 27.4 - - + -
146A ILE* 4.2 10.5 - - + -
150A ASN 3.4 15.9 - - - +
151A LEU* 5.1 2.7 - - + +
152A GLN* 5.0 1.5 - - - +
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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