Contacts of the strand formed by residues 304 - 309 (chain U) 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 U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30U ALA* 4.7 25.6 - - + +
34U ARG* 4.2 17.9 - - - +
50U PRO* 4.4 14.8 - - + -
51U LYS 4.2 18.4 - - - +
52U ASN* 3.8 7.2 - - - +
53U ILE* 5.3 1.1 - - + +
70U LEU* 5.3 2.7 - - + -
252U GLY 2.7 17.5 + - - +
253U ILE* 3.2 16.9 - - + -
254U VAL 2.7 31.9 + - - -
303U ILE* 1.3 76.8 - - - +
305U PHE* 1.3 61.0 + - - +
306U ILE* 3.5 34.8 - - + -
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Residues in contact with PHE 305 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52U ASN* 2.5 42.7 + - + +
53U ILE 3.0 25.6 + - - +
99U ILE* 5.8 0.2 - - + -
100U ILE* 5.6 1.6 - - + -
254U VAL* 3.3 46.9 - - + +
256U ILE* 5.0 13.0 - - + -
285U LEU* 3.0 47.3 - - + -
286U VAL* 3.3 33.4 - - + -
300U THR 5.2 1.8 - - - -
303U ILE* 4.4 24.2 - - + -
304U LEU* 1.3 74.5 - - - +
306U ILE* 1.3 68.9 + - - +
307U ALA* 4.2 0.7 - - + -
327U LEU* 5.0 4.9 - - + -
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Residues in contact with ILE 306 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27U VAL* 5.0 7.0 - - + -
30U ALA* 6.2 0.9 - - + -
53U ILE* 3.3 23.8 - - + +
55U MET* 3.1 39.0 - - + -
67U ALA* 4.2 15.0 - - + -
70U LEU* 4.2 21.5 - - + -
253U ILE* 4.4 7.2 - - + -
254U VAL 2.7 11.6 + - - +
255U PHE* 3.0 20.5 - - + -
256U ILE* 2.9 23.4 + - - -
304U LEU* 3.5 22.9 - - + -
305U PHE* 1.3 79.4 - - - +
307U ALA* 1.3 59.4 + - - +
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Residues in contact with ALA 307 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53U ILE 2.9 7.7 + - - -
54U LEU* 3.2 27.2 - - + +
55U MET 2.7 31.6 + - - -
256U ILE* 3.4 24.5 - - + +
259U ILE* 4.1 20.4 - - + +
305U PHE* 4.2 1.1 - - + -
306U ILE* 1.3 75.6 - - - +
308U SER* 1.3 55.9 + - - +
327U LEU* 5.2 3.4 - - + -
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Residues in contact with SER 308 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55U MET* 3.6 7.0 - - - -
63U LYS* 2.9 28.3 + - - -
255U PHE* 3.8 19.0 - - - -
256U ILE 2.9 7.2 + - - +
257U ASP* 2.5 40.0 + - - -
258U GLU 3.1 2.2 + - - -
259U ILE* 3.0 26.9 + - - +
306U ILE 4.1 1.2 + - - -
307U ALA* 1.3 75.0 - - - +
309U GLY* 1.3 57.1 + - - +
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Residues in contact with GLY 309 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55U MET 2.9 12.0 + - - +
56U ILE* 3.5 4.0 - - - +
57U GLY 3.1 25.2 + - - -
63U LYS* 3.9 4.0 - - - +
258U GLU* 4.6 2.9 - - - -
259U ILE* 4.6 0.2 - - - -
260U ASP* 3.0 15.7 - - - -
308U SER* 1.3 77.4 - - - +
310U ALA* 1.3 63.7 + - - -
311U PHE* 3.3 14.0 - - - +
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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