Contacts of the strand formed by residues 253 - 257 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31T LEU* 5.7 2.5 - - + -
34T ARG* 4.1 16.2 - - - +
67T ALA 4.5 1.3 - - - +
70T LEU* 3.1 45.3 - - + +
71T ALA* 4.7 2.7 - - + -
76T ALA* 4.6 12.3 - - + -
77T PRO 3.0 16.0 + - - +
78T PHE* 3.5 28.0 - - + -
79T ILE 3.4 21.8 + - - -
103T LEU* 3.8 4.2 - - - +
252T GLY* 1.3 78.3 - - - +
254T VAL* 1.3 65.2 + - - +
303T ILE* 4.1 0.2 - - - +
304T LEU* 3.2 22.0 - - + +
306T ILE* 4.4 11.7 - - + -
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Residues in contact with VAL 254 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79T ILE* 3.8 9.9 - - + +
81T VAL* 4.7 6.5 - - + -
99T ILE* 3.4 33.4 - - + -
100T ILE* 5.1 2.0 - - + -
103T LEU* 4.2 12.6 - - + -
253T ILE* 1.3 77.3 - - - +
255T PHE* 1.3 59.2 + - - +
256T ILE* 4.2 5.7 + - + +
303T ILE* 3.7 20.4 - - + -
304T LEU 2.7 9.9 + - - +
305T PHE* 3.3 41.0 - - + +
306T ILE* 2.7 33.3 + - - +
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Residues in contact with PHE 255 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55T MET* 3.4 2.9 - - + -
63T LYS 2.9 33.9 - - - -
64T THR* 2.9 30.7 - - + -
67T ALA* 3.5 15.3 - - + -
78T PHE* 3.9 16.2 - + + -
79T ILE 2.9 15.9 + - - +
80T LYS* 3.3 27.9 - - + -
81T VAL* 2.7 35.4 + - - +
253T ILE 4.1 0.2 + - - -
254T VAL* 1.3 74.8 - - - +
256T ILE* 1.3 58.6 + - - +
257T ASP* 3.8 3.0 + - + -
306T ILE* 3.0 44.0 - - + -
308T SER* 3.8 24.5 - - - -
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Residues in contact with ILE 256 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81T VAL* 3.6 21.3 - - + +
83T ALA* 4.8 12.1 - - + -
99T ILE* 5.8 1.1 - - + -
254T VAL* 4.8 9.6 - - + +
255T PHE* 1.3 74.3 - - - +
257T ASP* 1.3 68.2 + - - +
259T ILE* 4.4 24.0 + - + -
262T ILE* 6.1 0.2 - - + -
282T LEU* 3.5 31.9 - - + -
286T VAL* 5.6 5.4 - - + -
305T PHE* 5.0 17.0 - - + -
306T ILE 2.9 11.2 + - - +
307T ALA* 3.3 15.9 - - + +
308T SER 2.8 25.3 + - - +
323T LEU* 6.5 0.7 - - + -
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Residues in contact with ASP 257 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283S LEU* 5.4 3.1 - - - +
287S GLU* 5.3 2.4 - - - +
322S GLU* 5.4 1.0 - - - +
64T THR* 4.0 4.4 + - - -
80T LYS* 4.2 24.4 + - + -
81T VAL 3.0 18.7 + - - +
82T GLU* 3.5 23.7 - - + +
83T ALA 4.0 4.9 + - - -
255T PHE* 3.8 5.0 + - + -
256T ILE* 1.3 75.2 - - - +
258T GLU* 1.3 83.9 + - - +
308T SER* 2.5 25.6 + - - -
457T ATP 2.7 39.9 + - - -
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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