Contacts of the strand formed by residues 107 - 117 (chain A) in PDB entry 3AS2
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 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A GLN 3.9 0.6 + - - -
106A GLY* 1.3 74.0 - - - -
108A LEU* 1.3 66.5 + - - +
109A TYR* 3.7 10.6 - - - -
131A ILE 2.8 35.2 + - - +
137A SER* 3.7 22.1 + - - -
138A HIS* 4.0 3.6 - - - +
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Residues in contact with LEU 108 (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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83A ASP* 4.4 3.5 - - - +
107A GLY* 1.3 74.9 - - - +
109A TYR* 1.4 67.4 + - - +
128A GLU* 3.9 33.4 - - - +
129A ILE 3.5 3.4 - - - +
130A THR* 3.3 38.4 - - + +
137A SER 4.8 0.8 + - - +
138A HIS* 3.6 28.7 - - + +
140A LYS* 4.4 26.2 - - - +
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Residues in contact with TYR 109 (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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82A PHE* 3.9 36.1 - + + -
83A ASP* 3.3 23.3 - - + +
103A TYR* 3.9 20.6 - + - -
105A GLN* 3.1 42.6 + - - +
106A GLY 3.1 12.0 + - - -
107A GLY* 3.7 24.9 - - - -
108A LEU* 1.4 75.5 - - - +
110A GLN* 1.3 62.7 + - - +
128A GLU* 3.4 4.1 - - - +
129A ILE* 2.8 44.9 + - + +
131A ILE* 4.3 11.2 - - + -
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Residues in contact with GLN 110 (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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81A TYR 3.6 0.7 - - - +
82A PHE* 3.4 3.1 - - - -
83A ASP* 2.8 45.4 + - - +
84A GLY 4.7 0.5 + - - -
109A TYR* 1.3 69.4 - - - +
111A MET* 1.3 62.6 + - - +
112A GLU* 5.0 4.1 - - + +
126A PRO* 3.7 30.4 - - + +
127A VAL* 3.7 3.1 + - - -
128A GLU* 3.8 34.3 + - - +
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Residues in contact with MET 111 (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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28A ILE* 4.3 10.0 - - + +
36A LEU* 4.1 16.2 - - + -
65A VAL* 3.9 37.9 - - + -
80A VAL* 3.9 22.4 - - + -
81A TYR 3.2 11.9 - - - +
82A PHE* 4.0 4.7 - - + -
101A PHE* 5.3 0.4 - - - -
109A TYR 3.5 1.2 + - - -
110A GLN* 1.3 74.3 - - - +
112A GLU* 1.3 68.0 + - - +
113A ILE* 4.3 6.3 - - + -
124A SER* 4.5 0.3 + - - -
125A ALA 4.1 0.9 - - - +
126A PRO* 3.2 4.2 - - - +
127A VAL* 2.8 60.3 + - + +
129A ILE* 4.0 26.5 - - + -
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Residues in contact with GLU 112 (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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81A TYR* 2.9 48.3 + - + +
84A GLY* 4.6 12.1 + - - -
110A GLN* 4.0 3.7 + - - +
111A MET* 1.3 80.7 - - - +
113A ILE* 1.3 66.0 + - - +
114A GLU 4.2 0.2 - - - -
123A LYS* 3.9 36.0 - - + +
124A SER* 3.5 18.9 - - - +
126A PRO* 3.7 29.3 - - + +
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Residues in contact with ILE 113 (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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26A PRO* 3.5 16.0 - - + +
28A ILE* 3.8 21.5 - - + -
65A VAL* 3.7 32.3 - - + -
67A PHE* 3.7 34.1 - - + -
78A TYR* 4.4 3.6 - - + -
79A ASN 3.4 8.5 - - - +
80A VAL* 4.0 25.4 - - + -
99A ALA* 5.0 0.9 - - + -
111A MET* 4.3 10.3 - - + -
112A GLU* 1.3 79.7 - - - +
114A GLU* 1.3 65.2 + - - +
123A LYS* 4.3 1.1 - - - -
124A SER* 2.7 36.7 + - - -
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Residues in contact with GLU 114 (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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26A PRO* 4.2 2.9 - - - -
78A TYR* 3.1 9.9 - - - +
79A ASN* 2.8 52.3 + - - +
81A TYR* 2.8 29.5 + - + -
113A ILE* 1.3 74.7 - - - +
115A ALA* 1.4 57.1 + - - +
116A CYS* 3.7 6.1 - - - -
121A CYS* 3.5 33.1 - - + +
122A SER 3.3 9.6 - - - +
123A LYS* 3.1 35.8 + - + +
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Residues in contact with ALA 115 (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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23A PRO* 3.5 9.3 - - + +
24A THR 3.9 8.5 - - - +
26A PRO* 3.9 8.0 - - + +
69A GLN* 3.2 31.6 - - - +
74A SER 3.6 9.2 - - - +
77A THR 3.4 5.2 - - - -
92A ILE* 3.7 9.9 - - + -
114A GLU* 1.4 72.8 - - - +
116A CYS* 1.3 62.8 + - - +
121A CYS* 3.1 1.4 - - - -
122A SER 2.8 36.6 + - - +
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Residues in contact with CYS 116 (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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23A PRO* 3.6 4.3 - - - -
74A SER 4.9 0.2 + - - -
76A ASP* 2.9 31.6 + - - +
77A THR* 2.8 27.8 + - + +
79A ASN* 3.8 16.4 - - - -
114A GLU* 3.7 11.7 - - - -
115A ALA* 1.3 76.8 - - - +
117A ASP* 1.3 64.1 + - - +
120A GLY 3.3 4.0 - - - +
121A CYS* 2.2 45.3 - - - -
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Residues in contact with ASP 117 (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 ALA* 4.1 4.7 - - - +
23A PRO* 3.6 19.4 - - - +
73A THR* 4.8 5.0 + - - -
75A GLY* 4.0 15.4 - - - -
76A ASP* 3.8 14.1 - - - +
116A CYS* 1.3 77.9 - - - +
118A ALA* 1.3 64.4 + - - +
119A THR* 2.7 47.2 + - - +
120A GLY* 2.9 22.4 + - - +
121A CYS* 5.5 0.3 - - - -
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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