Contacts of the strand formed by residues 143 - 148 (chain A) in PDB entry 6N8P
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 LEU 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A PRO* 4.0 0.3 - - - +
138A HIS* 3.1 37.4 + - + +
140A SER* 4.3 3.2 + - - +
141A CYS* 3.8 0.7 - - - -
142A GLU* 1.3 93.2 + - + +
144A LEU* 1.3 66.9 + - - +
145A TYR* 3.3 39.7 - - + +
155A VAL* 3.8 20.4 - - + -
156A VAL 3.4 2.2 - - - -
157A GLN* 4.2 18.2 - - + -
158A LEU* 4.3 5.0 - - - +
164A LEU* 4.2 8.3 - - + -
167A ARG* 3.9 23.6 - - - +
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Residues in contact with LEU 144 (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 LEU* 5.1 0.2 - - + -
89A VAL* 4.0 32.1 - - + -
97A LEU* 4.2 17.3 - - + -
135A VAL* 4.1 13.0 - - + -
136A LEU 3.7 2.0 - - - +
137A PRO* 3.7 34.3 - - + -
143A LEU* 1.3 73.0 - - - +
145A TYR* 1.3 61.7 + - - +
146A LEU* 3.6 12.6 - - + +
154A PHE 3.4 2.3 - - - +
155A VAL* 3.4 4.7 - - - -
156A VAL* 2.6 49.7 + - + +
158A LEU* 3.6 25.8 - - + -
161A PHE* 4.6 11.0 - - + -
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Residues in contact with TYR 145 (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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135A VAL* 3.6 1.0 - - - -
136A LEU* 2.7 66.2 + - + -
138A HIS* 4.0 21.7 + + + -
143A LEU* 3.3 41.0 - - + +
144A LEU* 1.3 74.6 - - - +
146A LEU* 1.3 59.8 + - - +
153A VAL* 4.2 8.1 - - + -
154A PHE 3.5 2.0 - - - -
155A VAL* 3.6 26.9 - - + +
167A ARG* 5.0 3.5 + - - +
169A ILE* 4.7 2.2 - - + -
194A LEU* 3.4 15.9 - - + +
204A ILE* 4.0 16.4 - - + -
218A LEU* 3.2 43.5 - - + +
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Residues in contact with LEU 146 (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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97A LEU* 3.7 17.0 - - + -
117A PHE* 4.5 1.8 - - + -
119A LEU* 4.3 15.9 - - + -
132A ILE* 3.6 41.1 - - + -
134A VAL 3.5 3.8 - - - +
135A VAL* 4.1 13.5 - - + -
144A LEU* 3.6 29.4 - - + +
145A TYR* 1.3 79.5 - - - +
147A GLY* 1.3 62.1 + - - +
148A THR* 4.3 2.4 - - - +
152A ASN 3.6 1.4 - - - +
153A VAL* 3.2 5.0 - - - +
154A PHE* 2.8 42.1 + - + +
156A VAL* 3.7 20.2 - - + -
194A LEU* 4.0 2.5 - - - -
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Residues in contact with GLY 147 (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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132A ILE* 3.3 6.1 - - - +
133A THR* 2.5 41.9 + - - -
134A VAL 2.8 15.0 + - - -
146A LEU* 1.3 73.5 - - - +
148A THR* 1.3 54.6 - - - -
152A ASN 4.0 3.6 - - - -
153A VAL* 4.5 2.0 - - - -
191A VAL* 4.0 19.5 - - - -
194A LEU* 3.5 9.0 - - - +
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Residues in contact with THR 148 (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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119A LEU* 3.9 17.7 - - + -
129A ALA 3.5 10.7 + - - -
130A THR* 3.8 25.6 - - - +
131A GLN 3.2 9.6 - - - +
132A ILE* 4.3 2.7 - - + -
133A THR* 3.7 4.9 - - - -
146A LEU 4.3 2.5 - - - +
147A GLY* 1.3 78.8 - - - +
149A GLU* 1.3 64.5 + - - +
150A SER* 3.2 17.2 + - - -
151A GLY 3.5 4.3 + - - -
152A ASN* 2.7 22.8 + - - -
154A PHE* 3.9 12.7 - - + -
191A VAL* 3.2 23.3 + - - +
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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