Contacts of the strand formed by residues 53 - 56 (chain A) 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 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ALA* 3.9 8.1 - - + +
27A VAL* 3.6 40.4 - - + +
30A ALA* 4.0 11.0 - - + -
51A LYS 4.2 1.1 - - - +
52A ASN* 1.3 77.4 - - - +
54A LEU* 1.3 61.7 + - - +
55A MET* 4.1 8.7 - - + -
304A LEU* 5.1 3.6 - - + -
305A PHE 3.0 7.2 + - - +
306A ILE* 3.3 18.4 - - + -
307A ALA* 2.8 32.4 + - - +
327A LEU* 4.2 4.7 - - - +
329A ILE* 3.4 31.0 - - + +
331A VAL* 3.6 26.5 - - + -
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ILE* 1.3 78.6 - - - +
55A MET* 1.3 59.7 + - - +
56A ILE* 3.3 25.4 - - + +
259A ILE* 4.2 7.6 - - + -
307A ALA* 3.1 33.2 - - + +
308A SER 4.2 0.9 - - - +
311A PHE* 4.1 20.6 - - + -
316A PRO* 3.6 28.5 - - + -
319A LEU* 4.6 3.8 - - + -
327A LEU* 4.2 19.9 - - + +
329A ILE 2.8 5.8 + - - +
330A ARG* 3.4 21.8 - - - +
331A VAL* 3.0 25.6 + - - +
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Residues in contact with MET 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA* 5.0 7.0 - - + +
27A VAL* 3.9 24.9 - - + -
53A ILE* 4.2 3.8 - - + -
54A LEU* 1.3 73.8 - - - +
56A ILE* 1.3 62.7 - - - +
63A LYS* 3.7 43.6 - - + +
66A ILE* 4.5 8.7 - - + -
67A ALA* 4.6 2.0 - - + -
255A PHE* 4.5 1.6 - - + -
306A ILE* 3.2 36.3 - - + -
307A ALA 2.8 6.8 + - - +
308A SER* 3.1 5.2 - - - -
309A GLY 3.1 23.0 + - - -
331A VAL* 3.3 17.7 - - + -
333A LEU* 3.7 19.7 - - + -
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Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.3 43.5 - - + +
55A MET* 1.3 71.6 - - - +
57A GLY* 1.3 61.7 + - - +
63A LYS* 3.9 0.4 - - - -
309A GLY 3.1 4.3 - - - +
310A ALA 3.8 18.6 - - - +
311A PHE* 3.7 22.2 - - + -
316A PRO* 4.1 12.1 - - + -
330A ARG* 4.6 7.4 - - + -
331A VAL 3.1 13.4 + - - +
332A GLU* 3.5 17.3 - - + +
333A LEU* 2.8 25.5 + - - +
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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