Contacts of the strand formed by residues 304 - 309 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30S ALA* 4.7 25.4 - - + +
34S ARG* 4.2 17.5 - - - +
50S PRO* 4.4 15.3 - - + -
51S LYS 4.1 17.9 - - - +
52S ASN* 3.8 9.4 - - - +
53S ILE* 5.3 1.1 - - + +
70S LEU* 5.3 2.0 - - + -
252S GLY 2.7 17.4 + - - +
253S ILE* 3.2 16.2 - - + -
254S VAL 2.7 32.2 + - - -
303S ILE* 1.3 76.9 - - - +
305S PHE* 1.3 58.2 + - - +
306S ILE* 3.6 34.3 - - + -
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Residues in contact with PHE 305 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52S ASN* 2.5 42.9 + - + +
53S ILE 3.0 25.8 + - - +
99S ILE* 5.8 0.4 - - + -
100S ILE* 5.6 1.8 - - + -
254S VAL* 3.3 46.2 - - + +
256S ILE* 5.0 13.0 - - + -
285S LEU* 3.1 47.3 - - + -
286S VAL* 3.3 30.7 - - + -
300S THR 5.2 1.8 - - - -
303S ILE* 4.4 25.1 - - + -
304S LEU* 1.3 74.5 - - - +
306S ILE* 1.3 68.2 + - - +
307S ALA* 4.2 1.1 - - + +
327S LEU* 5.0 4.7 - - + -
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Residues in contact with ILE 306 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27S VAL* 5.0 6.7 - - + -
53S ILE* 3.3 22.9 - - + +
55S MET* 3.2 38.1 - - + -
67S ALA* 4.2 14.4 - - + -
70S LEU* 4.1 21.3 - - + -
253S ILE* 4.4 7.9 - - + -
254S VAL 2.7 11.3 + - - +
255S PHE* 3.0 20.0 - - + -
256S ILE* 2.9 23.3 + - - -
304S LEU* 3.6 23.8 - - + -
305S PHE* 1.3 81.4 - - - +
307S ALA* 1.3 60.9 + - - +
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Residues in contact with ALA 307 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53S ILE 2.9 7.5 + - - -
54S LEU* 3.2 27.1 - - + +
55S MET* 2.7 32.9 + - - +
256S ILE* 3.4 24.5 - - + +
259S ILE* 4.1 21.7 - - + +
305S PHE* 4.2 0.6 - - + -
306S ILE* 1.3 74.3 - - - +
308S SER* 1.3 55.4 + - - +
327S LEU* 5.2 3.8 - - + +
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Residues in contact with SER 308 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55S MET* 3.6 7.0 - - - -
63S LYS* 3.0 28.3 + - - -
255S PHE* 3.8 18.8 - - - -
256S ILE 2.9 7.0 + - - +
257S ASP* 2.5 39.1 + - - -
258S GLU 3.1 2.7 + - - -
259S ILE* 3.0 28.4 + - - +
306S ILE 4.1 1.2 + - - -
307S ALA* 1.3 74.5 - - - +
309S GLY* 1.3 56.1 + - - +
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Residues in contact with GLY 309 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55S MET 2.9 11.7 + - - +
56S ILE* 3.5 4.2 - - - +
57S GLY 3.1 25.9 + - - -
63S LYS* 3.9 3.6 - - - +
258S GLU* 4.6 3.1 - - - -
259S ILE* 4.4 0.7 - - - -
260S ASP* 3.0 15.7 - - - -
308S SER* 1.3 77.6 - - - +
310S ALA* 1.3 64.4 + - - -
311S PHE* 3.3 13.2 - - - +
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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