Contacts of the strand formed by residues 304 - 309 (chain F) 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 LEU 304 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30F ALA* 4.3 32.8 - - + +
31F LEU* 4.9 2.9 - - + +
34F ARG* 3.7 16.6 - - - +
50F PRO* 4.4 10.3 - - + -
51F LYS 4.7 3.1 - - - +
52F ASN* 3.6 22.7 - - - +
53F ILE* 4.7 3.4 - - + +
70F LEU* 4.4 13.9 - - + -
252F GLY 2.7 16.8 + - - +
253F ILE* 3.3 27.6 - - + +
254F VAL 2.9 26.2 + - - -
302F HIS 3.5 1.6 + - - -
303F ILE* 1.3 71.0 - - - +
305F PHE* 1.3 71.3 + - - +
306F ILE* 4.4 9.9 - - + -
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Residues in contact with PHE 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F ASN* 2.5 33.0 + - + +
53F ILE 3.0 23.9 + - - +
99F ILE* 5.1 0.4 - - + -
100F ILE* 4.5 9.2 - - + -
254F VAL* 3.4 40.2 - - + +
256F ILE* 4.4 13.2 - - + -
282F LEU* 6.4 0.4 - - + -
285F LEU* 4.1 21.8 - - + -
286F VAL* 3.7 47.1 - - + -
300F THR* 4.3 3.6 - - - -
303F ILE* 3.5 34.3 - - + -
304F LEU* 1.3 73.8 - - - +
306F ILE* 1.3 63.6 + - - +
307F ALA* 4.1 0.7 - - + -
327F LEU* 5.0 4.2 - - + +
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Residues in contact with ILE 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F VAL* 3.9 21.5 - - + -
53F ILE* 3.0 25.1 - - + +
55F MET* 3.2 34.1 - - + -
67F ALA* 4.1 16.2 - - + -
70F LEU* 4.3 6.3 - - + -
78F PHE* 5.8 0.4 - - + -
253F ILE* 3.7 24.7 - - + -
254F VAL 3.0 8.1 + - - +
255F PHE* 3.3 22.1 - - + -
256F ILE* 3.0 23.3 + - - -
304F LEU* 4.4 7.2 - - + -
305F PHE* 1.3 79.0 - - - +
307F ALA* 1.3 59.7 + - - +
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Residues in contact with ALA 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F ILE 2.7 11.4 + - - +
54F LEU* 3.2 19.0 - - + +
55F MET* 2.8 26.9 + - - +
256F ILE* 3.4 15.3 - - + +
259F ILE* 4.2 23.8 - - + -
305F PHE* 4.1 1.0 - - + -
306F ILE* 1.3 75.1 - - - +
308F SER* 1.3 60.8 + - - +
327F LEU* 4.2 15.0 - - + +
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Residues in contact with SER 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F MET* 3.3 7.4 - - - -
63F LYS* 3.8 16.8 - - - -
255F PHE* 3.5 25.4 - - - -
256F ILE 3.0 7.7 + - - -
257F ASP* 2.5 28.1 + - - -
258F GLU 3.4 1.4 + - - -
259F ILE* 2.9 31.6 + - - +
307F ALA* 1.3 76.5 - - - +
309F GLY* 1.3 61.1 + - - +
311F PHE* 4.5 1.6 - - - -
455F ATP 3.7 6.9 + - - -
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Residues in contact with GLY 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F MET 3.2 4.9 + - - -
56F ILE* 3.1 10.2 - - - -
57F GLY 2.9 22.0 + - - -
63F LYS* 4.2 5.8 - - - +
258F GLU* 4.4 4.3 - - - -
260F ASP* 3.3 16.8 - - - -
308F SER* 1.3 81.1 + - - +
310F ALA* 1.3 61.3 + - - -
311F PHE* 3.2 13.2 - - - -
455F ATP 6.0 0.4 - - - -
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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