Contacts of the strand formed by residues 93 - 97 (chain B) in PDB entry 5M4G
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 SER 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ARG* 3.6 35.3 + - - -
75B PHE* 4.3 2.5 - - - -
85B VAL 3.4 7.9 - - - -
86B ILE* 4.6 1.6 - - - +
91B GLY 3.4 3.7 + - - -
92B LYS* 1.3 71.8 - - - +
94B THR* 1.3 65.0 + - - +
95B LEU 4.3 0.2 - - - -
122B ALA 4.8 0.2 + - - -
123B VAL* 3.3 15.6 - - - +
124B ASP* 2.9 45.0 + - - +
125B ASP 3.1 8.3 + - - -
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Residues in contact with THR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PHE* 4.3 3.8 - - - -
84B GLY* 3.4 3.8 - - - -
85B VAL* 2.9 50.3 + - - +
92B LYS* 4.2 12.1 + - - +
93B SER* 1.3 77.4 + - - +
95B LEU* 1.3 67.6 + - - +
96B PHE* 3.7 25.1 - - + -
125B ASP* 3.3 33.0 + - - +
127B GLN* 4.1 7.6 - - + -
135B VAL* 5.1 3.4 - - + -
139B GLN* 4.6 8.6 + - - -
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Residues in contact with LEU 95 (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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71B PHE* 4.2 12.8 - - + -
75B PHE* 4.7 7.9 - - + -
77B VAL* 3.7 24.2 - - + -
82B CYS* 4.2 9.0 - - + -
83B TYR 3.5 14.8 - - - +
84B GLY* 4.6 0.2 - - - -
93B SER 4.3 0.4 - - - -
94B THR* 1.3 73.9 - - - +
96B PHE* 1.3 60.1 + - - +
97B VAL* 3.9 22.4 - - + -
117B PHE* 4.4 7.9 - - + -
121B TYR* 3.7 36.3 - - + -
123B VAL* 4.1 18.1 - - + +
125B ASP 3.0 7.0 + - - +
126B VAL* 3.2 10.1 - - + +
127B GLN 3.0 24.8 + - - +
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Residues in contact with PHE 96 (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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82B CYS* 3.1 12.8 - - - +
83B TYR* 2.8 47.3 + - + +
85B VAL* 3.8 27.1 - - + -
94B THR* 3.7 26.9 - - + -
95B LEU* 1.3 74.9 - - - +
97B VAL* 1.3 61.8 + - - +
127B GLN* 3.1 24.2 - - + -
128B TYR 3.5 18.2 - - - -
129B VAL* 3.6 16.6 - - + +
132B ILE* 3.6 43.1 - - + -
135B VAL* 3.8 21.5 - - + -
136B LEU* 4.7 2.9 - - + -
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Residues in contact with VAL 97 (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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79B GLU* 6.4 0.2 - - + -
82B CYS* 4.1 8.3 - - - -
95B LEU* 3.9 26.7 - - + -
96B PHE* 1.3 78.2 - - - +
98B PRO* 1.3 81.0 - - + +
114B LYS* 4.6 2.5 - - + -
117B PHE* 4.0 40.6 - - + -
126B VAL* 4.1 11.9 - - + -
127B GLN 2.9 15.3 + - - +
128B TYR* 3.3 17.3 - - + -
129B VAL* 2.9 21.8 + - - -
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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