Contacts of the strand formed by residues 253 - 257 (chain B) in PDB entry 1G3I
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 ILE 253 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 5.5 6.7 - - + -
34B ARG* 3.0 32.1 - - - +
67B ALA 5.1 1.8 - - - +
70B LEU* 4.5 12.8 - - + -
71B ALA* 4.1 16.2 - - + -
74B ALA* 5.9 0.7 - - + -
76B ALA* 4.1 20.6 - - + -
77B PRO 3.0 5.4 + - - +
78B PHE* 3.4 21.1 - - + -
79B ILE* 3.4 21.0 + - - +
103B LEU* 4.2 0.2 - - - +
251B ASN 4.3 1.3 - - - +
252B GLY* 1.3 73.3 - - - +
254B VAL* 1.3 67.4 + - - +
255B PHE 4.2 0.2 - - - -
304B LEU* 3.3 20.6 - - + +
306B ILE* 3.6 31.6 - - + -
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Residues in contact with VAL 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ILE* 3.6 21.3 - - + +
81B VAL* 5.2 2.2 - - + -
99B ILE* 3.9 23.6 - - + -
100B ILE* 4.9 1.3 - - + -
103B LEU* 3.8 10.8 - - + -
253B ILE* 1.3 81.5 - - - +
255B PHE* 1.3 59.2 + - - +
256B ILE* 3.8 15.4 + - + -
303B ILE* 3.6 19.7 - - + -
304B LEU 2.8 8.0 + - - +
305B PHE* 3.5 33.0 - - + +
306B ILE* 2.7 33.4 + - - +
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Residues in contact with PHE 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B MET* 4.5 0.9 - - - -
63B LYS* 3.7 16.8 - - + -
64B THR* 3.2 35.2 - - + -
67B ALA* 3.6 15.3 - - + -
78B PHE* 3.4 27.1 - + + -
79B ILE 2.9 10.8 + - - +
80B LYS* 3.6 23.1 - - + -
81B VAL 3.1 24.7 + - - -
253B ILE 4.2 0.4 - - - -
254B VAL* 1.3 74.1 - - - +
256B ILE* 1.3 59.2 + - - +
257B ASP* 3.4 18.1 + - + -
306B ILE* 3.1 30.7 - - + -
308B SER* 3.5 29.6 - - - -
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Residues in contact with ILE 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 3.7 14.8 - - + +
83B ALA* 4.1 17.7 - - + -
99B ILE* 5.2 1.6 - - + -
254B VAL* 3.9 14.1 - - + -
255B PHE* 1.3 73.8 - - - +
257B ASP* 1.3 59.5 + - - +
259B ILE* 3.5 33.0 - - + -
282B LEU* 3.6 33.7 - - + -
286B VAL* 5.2 5.6 - - + -
305B PHE* 4.1 25.6 - - + -
306B ILE 2.8 11.1 + - - +
307B ALA* 3.9 6.2 - - + +
308B SER 3.0 25.1 + - - +
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Residues in contact with ASP 257 (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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80B LYS* 3.6 31.8 + - - -
81B VAL 2.9 15.0 + - - +
82B GLU* 4.0 16.1 - - - +
83B ALA* 3.1 21.2 + - - +
255B PHE* 3.4 8.6 + - + -
256B ILE* 1.3 70.6 - - - +
258B GLU* 1.3 86.8 + - - +
259B ILE 2.9 4.7 + - - -
308B SER* 2.6 28.8 + - - -
451B ATP 3.0 32.5 + - - -
322C GLU* 5.7 0.7 - - - +
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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
------------------------------------------------------------
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