Contacts of the strand formed by residues 143 - 149 (chain B) in PDB entry 5GGP
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 VAL 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A GLU* 3.4 36.1 - - - +
114B VAL* 5.6 0.7 - - + -
119B VAL* 3.7 31.2 - - + -
134B ILE* 4.2 2.5 - - + -
135B VAL 3.6 5.6 - - - +
136B LEU* 3.5 18.8 - - + -
141B GLY 3.5 2.4 + - - +
142B HIS* 1.3 91.9 + - - +
144B MET* 1.3 61.5 + - - +
145B ALA 3.8 9.4 - - - +
146B LYS* 3.7 26.7 - - + -
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Residues in contact with MET 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ASP* 3.5 6.8 - - - +
123A GLU* 2.9 24.8 + - - -
124A ALA* 3.2 30.4 + - + +
126A GLU* 5.3 1.3 - - + -
127A GLN* 4.0 16.4 - - + +
135B VAL* 2.7 25.0 + - + +
136B LEU 4.0 1.6 - - - -
137B ASN* 3.6 42.4 - - + +
142B HIS* 3.7 4.5 - - + +
143B VAL* 1.3 74.3 - - - +
145B ALA* 1.3 61.1 + - + +
171B ARG* 3.7 43.1 - - - +
303B NA 4.2 7.6 - - - -
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLU* 3.4 25.1 - - - +
122A ASP* 4.8 0.4 - - - -
133B VAL 4.5 0.9 - - - -
134B ILE* 3.5 3.3 - - - -
135B VAL* 3.0 33.8 + - + +
143B VAL* 3.7 2.9 - - - +
144B MET* 1.3 82.0 - - + +
146B LYS* 1.3 65.8 + - - +
147B ARG* 4.3 0.7 - - + -
163B PHE* 3.8 27.4 - - + -
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Residues in contact with LYS 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LYS* 5.5 5.4 - - - +
118A THR* 5.4 1.2 - - - +
121A GLU* 2.8 37.0 + - - +
123A GLU* 3.4 22.0 + - - +
119B VAL* 2.8 49.7 + - + +
120B LEU* 5.2 6.1 - - + -
133B VAL 3.7 4.7 - - - -
134B ILE* 4.4 10.8 - - + -
143B VAL* 3.7 13.0 - - + -
145B ALA* 1.3 79.3 - - - +
147B ARG* 1.3 61.3 + - - +
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Residues in contact with ARG 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A THR* 3.3 32.4 + - - +
119A VAL* 3.5 25.2 + - - +
120A LEU* 4.1 5.0 - - - +
121A GLU* 3.8 21.9 - - + +
146A LYS* 4.2 9.5 - - - +
132B HIS* 3.3 6.0 + - - +
133B VAL 2.8 33.7 + - - +
145B ALA* 4.8 0.7 - - + -
146B LYS* 1.3 83.0 - - - +
148B VAL* 1.3 63.4 + - - +
149B PHE* 3.4 44.0 - - + -
159B ALA* 5.3 4.2 + - - +
163B PHE* 3.6 43.9 - - + +
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A THR* 5.6 3.1 - - - +
118A THR* 5.0 13.2 - - - +
128B GLY* 3.9 10.1 - - - +
129B ARG 3.5 22.2 - - - +
131B ILE 3.4 8.3 - - - +
132B HIS* 3.5 42.4 - - + +
147B ARG* 1.3 77.5 + - - +
149B PHE* 1.3 72.6 + - - +
150B ASP 4.1 1.3 + - - +
156B GLU* 4.5 3.5 - - - +
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Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ARG 4.2 2.0 - - - -
131B ILE 2.9 41.0 + - - +
133B VAL* 4.2 9.2 - - + -
147B ARG* 3.4 47.1 - - + -
148B VAL* 1.3 77.4 - - - +
150B ASP* 1.3 59.4 + - - +
151B THR* 2.8 16.3 + - + -
156B GLU* 3.9 15.7 - - - +
159B ALA* 3.7 13.2 - - + -
160B MET* 3.5 53.4 - - + -
163B PHE* 3.5 38.8 - + + -
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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