Contacts of the strand formed by residues 304 - 309 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30E ALA* 4.3 22.9 - - + -
31E LEU* 5.0 5.4 - - + +
34E ARG* 3.5 15.9 - - - +
50E PRO* 4.3 11.2 - - + -
51E LYS 4.7 2.7 - - - +
52E ASN* 3.9 21.3 - - - +
53E ILE* 4.5 9.4 - - + -
70E LEU* 4.5 9.0 - - + -
252E GLY 2.7 15.8 + - - +
253E ILE* 3.3 27.3 - - + +
254E VAL 2.9 24.6 + - - -
302E HIS 3.4 2.8 + - - -
303E ILE* 1.3 72.7 - - - +
305E PHE* 1.3 79.8 + - - +
306E ILE* 4.3 10.5 - - + -
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Residues in contact with PHE 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E ASN* 2.4 49.1 + - + +
53E ILE 3.0 18.8 + - - +
100E ILE* 4.5 8.5 - - + -
254E VAL* 3.5 31.0 - - + -
256E ILE* 4.2 15.9 - - + -
282E LEU* 5.9 0.7 - - + -
285E LEU* 3.8 47.3 - - + -
286E VAL* 3.9 27.4 - - + -
300E THR* 4.3 2.7 - - - -
303E ILE* 3.3 38.6 - - + -
304E LEU* 1.3 72.1 - - - +
306E ILE* 1.3 64.4 + - - +
307E ALA* 4.1 1.1 - - + -
327E LEU* 5.2 4.5 - - + -
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Residues in contact with ILE 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E VAL* 3.7 24.7 - - + -
53E ILE* 3.2 22.2 - - + +
55E MET* 3.3 33.2 - - + -
67E ALA* 4.2 13.0 - - + -
70E LEU* 4.3 3.8 - - + -
253E ILE* 3.6 26.7 - - + -
254E VAL 2.8 8.5 + - - +
255E PHE* 3.2 22.6 - - + -
256E ILE* 2.8 25.6 + - - -
304E LEU* 4.3 8.3 - - + -
305E PHE* 1.3 80.8 - - - +
307E ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E ILE 2.7 12.0 + - - +
54E LEU* 3.2 18.9 - - + +
55E MET* 2.7 34.5 + - - +
255E PHE* 4.9 0.2 - - - -
256E ILE* 3.3 14.4 - - + +
259E ILE* 4.0 25.6 - - + -
305E PHE* 4.1 0.9 - - + -
306E ILE* 1.3 75.6 - - - +
308E SER* 1.3 55.1 + - - +
327E LEU* 4.2 13.6 - - + +
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Residues in contact with SER 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E LEU* 4.7 1.8 - - - -
55E MET* 3.2 8.5 - - - -
63E LYS* 3.7 18.3 - - - +
255E PHE* 3.5 23.3 - - - -
256E ILE 2.9 6.9 + - - -
257E ASP* 2.3 30.8 + - - -
258E GLU* 3.0 2.9 + - - +
259E ILE* 3.0 29.0 + - - +
307E ALA* 1.3 74.9 - - - +
309E GLY* 1.3 60.8 + - - +
454E ATP 3.6 4.5 + - - -
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Residues in contact with GLY 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E MET 3.2 4.8 + - - -
56E ILE* 3.2 3.5 - - - -
57E GLY 3.2 19.9 + - - -
63E LYS* 4.3 4.9 - - - +
258E GLU* 4.3 4.5 - - - -
260E ASP* 3.3 17.7 - - - -
308E SER* 1.3 79.7 + - - +
310E ALA* 1.3 64.8 + - - -
311E PHE* 3.1 19.6 - - - -
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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