Contacts of the strand formed by residues 140 - 146 (chain S) in PDB entry 5A0Q
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 ALA 140 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31S ILE* 4.0 22.6 - - + +
78S MET* 3.5 1.2 - - - -
79S SER* 3.0 36.6 + - - +
138S GLY 3.8 2.0 + - - -
139S VAL* 1.4 79.4 - - - +
141S LEU* 1.3 59.8 + - - +
155S HIS* 4.0 11.9 - - - +
156S MET 3.5 9.9 - - - +
158S PRO* 5.1 1.3 - - + -
170S ILE* 3.7 24.3 - - + +
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Residues in contact with LEU 141 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76S CYS* 4.0 13.2 - - - -
77S ALA 3.5 11.4 - - - +
78S MET* 4.1 7.9 - - + -
85S ALA* 4.7 2.0 - - + +
88S LEU* 4.5 15.0 - - + -
89S ILE* 4.5 11.7 - - + -
116S VAL* 3.8 29.4 - - + -
139S VAL* 3.6 25.6 - - + +
140S ALA* 1.3 75.8 - - - +
142S LEU* 1.3 62.5 + - - +
143S PHE* 3.6 26.2 - - + -
155S HIS* 3.4 8.5 - - - -
156S MET* 2.9 44.6 + - + -
170S ILE* 4.4 0.7 - - - -
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Residues in contact with LEU 142 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S ALA* 4.1 7.0 - - + +
38S ILE 4.0 9.2 - - - +
39S GLY* 3.7 25.1 - - - +
48S LEU* 3.4 20.3 - - + +
76S CYS* 4.3 0.9 - - - -
77S ALA* 3.0 37.9 + - + -
141S LEU* 1.3 78.3 - - - +
143S PHE* 1.3 64.2 + - - +
153S LEU* 4.2 16.2 - - + -
154S PHE 3.9 2.7 - - - -
155S HIS* 3.8 29.8 - - + -
168S ARG* 4.6 7.0 - - + +
170S ILE* 3.8 30.7 - - + -
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Residues in contact with PHE 143 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48S LEU* 4.5 0.4 - - - -
70S ILE* 4.6 2.2 - - + -
74S ILE* 4.0 10.3 - - + -
75S GLY 3.3 7.6 - - - +
76S CYS* 4.1 20.9 - - + +
88S LEU 6.0 0.2 - - - -
89S ILE* 6.5 0.2 - - - -
92S ALA* 4.5 9.6 - - + -
109S VAL* 3.9 13.9 - - + -
112S VAL* 3.8 32.1 - - + -
113S THR* 3.5 37.0 - - + +
116S VAL* 4.0 21.1 - - + -
141S LEU* 3.6 39.3 - - + -
142S LEU* 1.3 72.1 - - - +
144S GLY* 1.3 59.4 + - - +
145S GLY 4.1 0.2 - - - -
153S LEU* 3.7 7.4 - - - +
154S PHE 3.2 29.3 + - - +
156S MET* 4.3 5.2 - - + -
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Residues in contact with GLY 144 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46S VAL* 4.0 26.0 - - - +
48S LEU* 3.8 6.8 - - - +
73S HIS 3.8 0.5 - - - +
74S ILE* 3.3 2.4 - - - -
75S GLY* 2.6 39.2 + - - +
142S LEU 3.5 2.6 + - - -
143S PHE* 1.3 74.7 - - - +
145S GLY* 1.3 56.4 + - - -
152S GLN 3.8 9.2 - - - -
153S LEU* 4.5 1.8 - - - -
220S VAL* 5.0 2.1 - - - +
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Residues in contact with GLY 145 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46S VAL* 4.3 0.4 - - - +
73S HIS* 3.0 14.6 - - - -
74S ILE* 3.8 3.4 - - - -
109S VAL* 3.3 31.8 - - - +
143S PHE 4.1 0.2 - - - -
144S GLY* 1.3 75.5 - - - -
146S VAL* 1.3 65.0 + - - -
147S ASP* 3.5 2.9 + - - -
152S GLN* 3.3 26.5 + - - +
220S VAL* 5.9 0.4 - - - -
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Residues in contact with VAL 146 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44S GLU 5.1 0.9 - - - +
45S GLY* 4.8 2.5 - - - -
46S VAL* 3.8 21.5 - - + +
73S HIS* 3.3 24.3 + - - +
145S GLY* 1.3 68.4 - - - -
147S ASP* 1.3 60.7 + - - +
150S GLY* 3.7 26.2 - - - -
151S PRO* 3.8 7.0 - - + -
220S VAL* 3.7 38.6 - - + +
221S GLN 4.7 1.1 - - - +
222S PRO* 4.0 29.2 - - + +
224S GLN 6.0 0.4 - - - +
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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