Contacts of the strand formed by residues 151 - 157 (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 PRO 151 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41S GLN* 3.1 25.6 + - + +
42S THR 3.3 17.0 - - - +
43S SER* 3.2 43.5 - - - +
44S GLU 4.8 3.4 - - - +
45S GLY* 4.6 6.1 - - - +
46S VAL* 4.6 8.3 - - + -
146S VAL* 3.8 15.6 - - + -
149S LYS* 4.3 4.9 - - - +
150S GLY* 1.3 84.0 - - - +
152S GLN* 1.3 65.1 + - - +
164S GLN* 5.5 0.3 + - - -
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Residues in contact with GLN 152 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41S GLN* 4.3 5.6 - - - +
46S VAL* 3.8 5.4 - - - +
108S THR* 5.9 0.2 - - - -
109S VAL* 3.5 17.9 + - + +
110S GLU* 4.4 6.0 + - - +
144S GLY* 3.8 1.7 - - - -
145S GLY 3.3 31.8 + - - +
147S ASP* 2.5 41.1 + - - +
149S LYS* 4.0 23.4 - - + +
150S GLY 4.0 0.7 - - - +
151S PRO* 1.3 78.4 - - - +
153S LEU* 1.3 63.0 + - - +
154S PHE* 4.1 20.0 - - + -
164S GLN* 3.9 21.6 - - - +
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Residues in contact with LEU 153 (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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39S GLY 3.4 25.4 - - - +
40S ILE 3.3 26.9 - - - +
41S GLN* 4.0 21.3 + - + +
46S VAL* 4.6 9.2 - - + -
48S LEU* 3.7 20.2 - - + -
142S LEU* 4.2 22.0 - - + -
143S PHE 3.7 12.1 - - - +
144S GLY* 4.7 0.2 - - - -
152S GLN* 1.3 75.9 - - - +
154S PHE* 1.3 64.1 + - - +
155S HIS 4.5 1.1 - - - +
164S GLN* 5.2 1.2 - - - +
165S CYS* 2.9 46.7 + - + +
166S ASP 5.2 0.7 - - - +
168S ARG 5.1 1.6 - - - +
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Residues in contact with PHE 154 (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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109S VAL* 3.9 17.6 - - + +
110S GLU* 3.8 38.4 - - + -
113S THR* 3.5 22.0 - - + +
142S LEU* 3.9 0.4 - - - -
143S PHE* 3.2 35.2 + - - +
152S GLN* 4.1 18.2 - - + -
153S LEU* 1.3 82.9 - - - +
155S HIS* 1.4 59.9 + - - +
162S PHE* 3.6 34.1 - + - -
163S VAL 3.5 5.2 - - - +
164S GLN* 3.6 48.5 - - + -
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Residues in contact with HIS 155 (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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140S ALA* 4.0 9.3 - - + +
141S LEU 3.4 11.4 - - - -
142S LEU* 3.8 11.1 - - + +
153S LEU* 3.9 0.6 + - - +
154S PHE* 1.4 72.7 - - - +
156S MET* 1.3 73.3 + - - +
157S ASP* 3.3 42.6 + - - -
162S PHE* 3.5 3.8 - - - +
163S VAL* 3.0 37.5 + - + +
165S CYS* 3.3 26.2 - - - -
168S ARG* 4.0 21.2 + - + +
170S ILE* 3.2 34.1 - - + +
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Residues in contact with MET 156 (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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88S LEU* 5.1 5.4 - - + -
113S THR* 3.8 22.0 - - + +
116S VAL* 3.6 34.3 - - + +
117S SER* 3.5 35.7 - - - +
120S ALA* 4.6 11.4 - - + -
139S VAL 4.3 3.2 - - - +
140S ALA* 3.5 6.1 - - - -
141S LEU* 2.9 54.5 + - + +
143S PHE* 4.3 1.3 - - + -
154S PHE 4.0 0.2 + - - -
155S HIS* 1.3 77.4 + - - +
157S ASP* 1.4 84.2 + - - +
158S PRO* 4.8 3.6 - - + -
160S GLY* 5.0 0.7 - - - -
161S THR 3.7 6.5 - - - +
162S PHE* 4.1 1.1 - - + -
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Residues in contact with ASP 157 (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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28S ILE* 5.2 5.2 - - + +
139S VAL 4.4 0.2 - - - -
140S ALA* 5.4 0.2 - - - -
155S HIS* 3.3 29.6 + - - -
156S MET* 1.4 90.6 - - - +
158S PRO* 1.3 68.2 - - + +
159S SER* 3.1 16.8 + - - +
160S GLY 3.7 2.1 + - - -
161S THR* 3.0 35.6 + - - +
163S VAL* 4.1 11.3 - - - +
168S ARG* 5.5 2.9 + - - -
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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